Buyong Ma, Ph.D.
School of Pharmacy, Shanghai Jiaotong University.
E-mail: mabuyong@sjtu.edu.cn

Professional Career
2020 Professor | School of Pharmacy, Shanghai Jiao Tong University, China
2003-2020 Senior Scientist | Leidos Biomedical Research, Inc. NCI, Frederick, MD. USA
2002-2003 Scientist | Locus Pharmaceuticals, Inc; Philadelphia, PA, USA.
1998-2002 Research Fellow | Laboratory of Experimental and Computational Biology, CCR, NCI, NIH, Frederick, MD, USA.
1995-1998 Postdoctoral Research Associate | Computational Center for Molecular Structure and Design, University of Georgia, Athens, GA, USA.

Education
1991-1995 Ph.D. in Physical Chemistry | University of Georgia, Athens, GA, USA
1984-1987 M.S. in Polymer Chemistry | Hubei Research Institute of Chemistry, China
1980-1984 B.S. in Chemical Engineering | Hefei University of Technology, China

Research Interests
(1) Mechanism and drug design in cancer and protein aggregation diseases, including Alzheimer’s disease, Parkinson’s disease, Prion disease, Systemic light chain amyloidosis.
(2) Computational biology of cancer and immunology.
(3) Protein dynamics and function.
(4) Antibody/Antigen Design, Protein Engineering.

Research Achievements
More than 220 scientific publications, including more than twenty in PNAS、JACS、Chemical Review, Nature Communication, Nature Structural & Molecular Biology. (1) Established the popular theory of “Conformation selection” in biomolecular recognition, in complementary to traditional “Lock and key”and “Induced Fit”. (2) Delineated structure characteristic of hotspot in protein-protein interaction. (3) Pioneer in computational study of protein aggregation. The first to reveal atomic structure of amyloid.
Google Scholar
https://scholar.google.com/citations?hl=en&user=6VkxqHIAAAAJ&view_op=list_works&sortby=pubdate


Editor-in-Chief: BME Horizon, BioCHem, Proteins & Nucleic Acids: Therapeutics and Diagnostics
Associate Editor: Pharmaceutical Fronts
Editorial Board Member
Antibodies, Journal of Alzheimer's Disease and Related Diseases, Exploration of Immunology。

Complete publication list

1. Ma, B., Wang, Y., Li, X., Shen, C., Lin, H., Du, C., Yang, S., Zeng, R., Tang, X., Hu, J. et al. (2024) Recent Advancements in the Application of Artificial Intelligence in Drug Molecular Generation and Synthesis Planning. Pharmaceutical Fronts, 06, e394-e405.
2. Su, Y., Zeng, X., Zhang, L., Bian, Y., Wang, Y. and Ma, B. (2024) ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Abeta Antibodies and Peptides. Interdiscip Sci.
3. Tang, Y., Yu, M., Bai, G., Li, X., Xu, Y. and Ma, B. (2024) Deep learning of protein energy landscape and conformational dynamics from experimental structures in PDB. bioRxiv, 2024.2006.2027.600251.
4. Zhang, Y., Jin, Y., Wang, Y., Wang, S., Niu, Y., Ma, B. and Li, J. (2024) Insights of Expression Profile of Chemokine Family in Inflammatory Bowel Diseases and Carcinogenesis. Int J Mol Sci, 25.
5. Bai, G., Zeng, X., Zhang, L., Wang, Y. and Ma, B. (2024) Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b. Biochem Biophys Res Commun, 712-713, 149945.
6. Bai, J., Li, X., Zhao, J., Zong, H., Yuan, Y., Wang, L., Zhang, X., Ke, Y., Han, L., Xu, J. et al. (2024) Re-Engineering Therapeutic Anti-Abeta Monoclonal Antibody to Target Amyloid Light Chain. Int J Mol Sci, 25.
7. Wang, Y., Wang, S., Niu, Y., Ma, B. and Li, J. (2023) Data Mining Suggests That CXCL14 Gene Silencing in Colon Cancer Is Due to Promoter Methylation. Int J Mol Sci, 24.
8. Sun, C., Bai, G., Xu, H., Wang, Y. and Ma, B. (2023) SAGERank: Inductive Learning of Protein-Protein Interaction from Antibody-Antigen Recognition using Graph Sample and Aggregate Networks Framework. bioRxiv, 2023.2010.2011.561985.
9. Su, Y., Zhang, L., Wang, Y. and Ma, B. (2023) ABTrans: A Transformer-based model for predicting interaction between anti-Aß antibodies and peptides. bioRxiv, 2023.2010.2009.561503.
10. Zeng, X., Zhang, L., Ning, Z., Qiu, Y., Dong, R., Li, X., Lv, L., Xu, H., Wang, Y. and Ma, B. (2023) VirEvol platform : accurate prediction and visualization of SARS-CoV-2 evolutionary trajectory based on protein language model, structural information and immunological recognition mechanism. bioRxiv, 2023.2009.2015.557978.
11. Zeng, X., Wang, T., Kang, Y., Bai, G. and Ma, B. (2023) Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies' Recognition of TRBC1 and TRBC2. Antibodies (Basel), 12.
12. Zeng, X., Bai, G., Sun, C. and Ma, B. (2023) Recent Progress in Antibody Epitope Prediction. Antibodies (Basel), 12.
13. Chen, J., Li, J., Sun, X., Lu, H., Liu, K., Li, Z., Guan, J., Song, H., Wei, W., Ge, Y. et al. (2023) Precision Therapy of Recurrent Breast Cancer through Targeting Different Malignant Tumor Cells with a HER2/CD44-Targeted Hydrogel Nanobot. Small, e2301043.
14. Jia, Y., Ren, S., Song, L., Wang, S., Han, W., Li, J., Yu, Y. and Ma, B. (2023) PGLYRP1-mIgG2a-Fc inhibits macrophage activation via AKT/NF-kappaB signaling and protects against fatal lung injury during bacterial infection. iScience, 26, 106653.
15. Qu, H., Chen, H., Cheng, W., Wang, Y., Xia, Y., Zhang, L., Ma, B., Hu, R. and Xue, X. (2023) A supramolecular assembly strategy for hydrophilic drug delivery towards synergistic cancer treatment. Acta Biomater.
16. Ding, J., Lee, Y.T., Bhandari, Y., Schwieters, C.D., Fan, L., Yu, P., Tarosov, S.G., Stagno, J.R., Ma, B., Nussinov, R. et al. (2023) Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun, 14, 714.
17. Kabir, K.L., Ma, B., Nussinov, R. and Shehu, A. (2022) Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody. Biomolecules, 12.
18. Tsuji, K., Hymel, D., Ma, B., Tamamura, H., Nussinov, R. and Burke, T.R., Jr. (2022) Development of ultra-high affinity bivalent ligands targeting the polo-like kinase 1. RSC Chem Biol, 3, 1111-1120.
19. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2019) Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods Mol Biol, 1851, 317-335.
20. Lucchesi, C.A., Zhang, J., Ma, B., Chen, M. and Chen, X. (2018) Disruption of the Rbm38-eIF4E complex with a synthetic peptide Pep8 increases p53 expression. Cancer Res.
21. Lei, J., Qi, R., Tang, Y., Wang, W., Wei, G., Nussinov, R. and Ma, B. (2018) Conformational stability and dynamics of the cancer-associated isoform Delta133p53beta are modulated by p53 peptides and p53-specific DNA. FASEB J, fj201801973R.
22. Zhao, J., Nussinov, R. and Ma, B. (2018) Antigen binding allosterically promotes Fc receptor recognition. MAbs, 1-17.
23. Weismiller, H.A., Murphy, R., Wei, G., Ma, B., Nussinov, R. and Margittai, M. (2018) Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms. J Biol Chem, 293, 17336-17348.
24. Rangarajan, S., He, Y., Chen, Y., Kerzic, M.C., Ma, B., Gowthaman, R., Pierce, B.G., Nussinov, R., Mariuzza, R.A. and Orban, J. (2018) Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. J Biol Chem, 293, 15991-16005.
25. Li, X., Dong, X., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2018) The distinct structural preferences of tau protein repeat domains. Chem Commun (Camb), 54, 5700-5703.
26. Song, N.Y., Zhu, F., Wang, Z., Willette-Brown, J., Xi, S., Sun, Z., Su, L., Wu, X., Ma, B., Nussinov, R. et al. (2018) IKKalpha inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways. Proc Natl Acad Sci U S A, 115, E812-E821.
27. Qi, R., Wei, G., Ma, B. and Nussinov, R. (2018) Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example. Methods Mol Biol, 1777, 101-119.
28. Qian, Z., Zou, Y., Zhang, Q., Chen, P., Ma, B., Wei, G. and Nussinov, R. (2018) Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition. Biochim Biophys Acta, s0005-2736, 30046-30044.
29. Ren, B., Hu, R., Zhang, M., Liu, Y., Xu, L., Jiang, B., Ma, J., Ma, B., Nussinov, R. and Zheng, J. (2018) Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies. Methods Mol Biol, 1777, 429-447.
30. Zhao, J., Zhang, B., Zhu, J., Nussinov, R. and Ma, B. (2017) Structure and energetic basis of overrepresented lambda light chain in systemic light chain amyloidosis patients. Biochim Biophys Acta, 1864, 2294-2303.
31. Zhao, J., Nussinov, R. and Ma, B. (2017) Mechanisms of recognition of Abeta monomer, oligomer, and fibril by homologous antibodies. J Biol Chem, 44, 18325-18343.
32. Wang, M., Zhu, D., Zhu, J., Nussinov, R. and Ma, B. (2017) Local and global anatomy of antibody-protein antigen recognition. J Mol Recognit, 21, e2693.
33. Dong, X., Sun, Y., Wei, G., Nussinov, R. and Ma, B. (2017) Binding of protofibrillar Abeta trimers to lipid bilayer surface enhances Abeta structural stability and causes membrane thinning. Phys Chem Chem Phys, 19, 27556-27569.
34. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2017) Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer. J Mol Biol, 429, 3925-3941.
35. Libardo, M.D.J., Bahar, A.A., Ma, B., Fu, R., McCormick, L.E., Zhao, J., McCallum, S.A., Nussinov, R., Ren, D., Angeles-Boza, A.M. et al. (2017) Nuclease Activity Gives an Edge to Host-Defense Peptide Piscidin 3 over Piscidin 1, Rendering it more Effective against Persisters and Biofilms. FEBS J.
36. Zhang, M., Zheng, J., Nussinov, R. and Ma, B. (2017) Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane. Sci Rep, 7, 2635.
37. Xu, L., Ma, B., Nussinov, R. and Thompson, D. (2017) Familial Mutations May Switch Conformational Preferences in alpha-Synuclein Fibrils. ACS Chem Neurosci, 8, 837-849.
38. Zhao, J., Nussinov, R. and Ma, B. (2017) Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel, 30, 67-76.
39. Gong, Y., Zhu, Y., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2017) Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity. J Phys Chem B, 121, 508-517.
40. Gan, W., Schneidman, D., Zhang, N., Ma, B. and Nussinov, R. (2017) Probing Oligomerized Conformations of Defensin in the Membrane. Methods Mol Biol, 1529, 353-362.
41. Zou, Y., Sun, Y., Zhu, Y., Ma, B., Nussinov, R. and Zhang, Q. (2016) Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci, 7, 286-296.
42. Zhu, Y., Ma, B., Qi, R., Nussinov, R. and Zhang, Q. (2016) Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations. J Phys Chem B, 120, 3551-3559.
43. Zhan, C., Qi, R., Wei, G., Guven-Maiorov, E., Nussinov, R. and Ma, B. (2016) Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization. Protein Eng Des Sel, 29, 347-354.
44. Maximova, T., Moffatt, R., Ma, B., Nussinov, R. and Shehu, A. (2016) Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol, 12, e1004619.
45. Ma, B., Zhao, J. and Nussinov, R. (2016) Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. Biochim Biophys Acta, 1860, 2672-2681.
46. Zhao, J., Ma, B. and Nussinov, R. (2016) Compilation and Analysis of Enzymes, Engineered Antibodies, and Nanoparticles Designed to Interfere with Amyloid-β Aggregation. Israel Journal of Chemistry, 57, 622-633.
47. Ma, B. and Nussinov, R. (2016) Protein dynamics: Conformational footprints. Nat Chem Biol, 12, 890-891.
48. Zhang, M., Zheng, J., Nussinov, R. and Ma, B. (2016) Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane. Sci Rep, 6, 33340.
49. Lei, J., Qi, R., Wei, G., Nussinov, R. and Ma, B. (2016) Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Phys Chem Chem Phys, 18, 8098-8107.
50. Hewitt, W.M., Lountos, G.T., Zlotkowski, K., Dahlhauser, S.D., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B. et al. (2016) Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angew Chem Int Ed Engl, 55, 5703-5707.
51. Xu, L., Nussinov, R. and Ma, B. (2016) Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the alpha-synuclein fibrils. Eur J Med Chem, 121, 841-850.
52. Xu, L., Zheng, J., Margittai, M., Nussinov, R. and Ma, B. (2016) How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability? ACS Chem Neurosci, 7, 565-575.
53. Xu, L., Nussinov, R. and Ma, B. (2016) Allosteric stabilization of the amyloid-beta peptide hairpin by the fluctuating N-terminal. Chem Commun (Camb), 52, 1733-1736.
54. Wei, G., Xi, W., Nussinov, R. and Ma, B. (2016) Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev, 116, 6516-6551.
55. Zhu, Y., Yang, S., Qi, R., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2015) Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein. J Phys Chem B, 119, 14236-14244.
56. Datta, S.A., Clark, P.K., Fan, L., Ma, B., Harvin, D.P., Sowder, R.C., 2nd, Nussinov, R., Wang, Y.X. and Rein, A. (2015) Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly. J Virol, 90, 1773-1787.
57. Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R. and Ishii, Y. (2015) Abeta(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease. Nat Struct Mol Biol, 22, 499-505.
58. Clausen, R., Ma, B., Nussinov, R. and Shehu, A. (2015) Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput Biol, 11, e1004470.
59. Baram, M., Atsmon-Raz, Y., Ma, B., Nussinov, R. and Miller, Y. (2015) Amylin-Abeta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. Phys Chem Chem Phys.
60. Qi, R., Luo, Y., Wei, G., Nussinov, R. and Ma, B. (2015) Aβ “Stretching-and-Packing” Cross-Seeding Mechanism Can Trigger Tau Protein Aggregation. The Journal of Physical Chemistry Letters, 6, 3276-3282.
61. Xu, L., Shan, S., Chen, Y., Wang, X., Nussinov, R. and Ma, B. (2015) Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Abeta40 Peptide Oligomerization. J Chem Inf Model, 55, 1218-1230.
62. Zhou, P., Zhang, N., Nussinov, R. and Ma, B. (2015) Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. J Comput Biol, 22, 876-886.
63. Fetics, S.K., Guterres, H., Kearney, B.M., Buhrman, G., Ma, B., Nussinov, R. and Mattos, C. (2015) Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. Structure, 23, 505-516.
64. Miller, Y., Ma, B. and Nussinov, R. (2015) Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity. J Phys Chem B, 119, 482-490.
65. Cronin, M., Coolbaugh, M.J., Nellis, D., Zhu, J., Wood, D.W., Nussinov, R. and Ma, B. (2015) Dynamics differentiate between active and inactive inteins. Eur J Med Chem, 91, 51-62.
66. Zhu, Y., Wu, Y., Luo, Y., Zou, Y., Ma, B. and Zhang, Q. (2014) R102Q mutation shifts the salt-bridge network and reduces the structural flexibility of human neuronal calcium sensor-1 protein. J Phys Chem B, 118, 13112-13122.
67. Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q. and Nussinov, R. (2014) Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors, 32, 236-246.
68. Huang, Q., Yu, L., Levine, A.J., Nussinov, R. and Ma, B. (2014) Dipeptide analysis of p53 mutations and evolution of p53 family proteins. Biochim Biophys Acta, 1844, 198-206.
69. Nussinov, R., Ma, B. and Tsai, C.J. (2014) Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys Chem, 186, 22-30.
70. Ma, B. and Nussinov, R. (2014) Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des, 20, 1293-1301.
71. Qi, R., Luo, Y., Ma, B., Nussinov, R. and Wei, G. (2014) Conformational distribution and alpha-helix to beta-sheet transition of human amylin fragment dimer. Biomacromolecules, 15, 122-131.
72. Meyer, V., Dinkel, P.D., Luo, Y., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R., Eaton, S.S. et al. (2014) Single mutations in tau modulate the populations of fibril conformers through seed selection. Angew Chem Int Ed Engl, 53, 1590-1593.
73. Luo, Y., Ma, B., Nussinov, R. and Wei, G. (2014) Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. J Phys Chem Lett, 5, 3026-3031.
74. Ji, X., Huang, Q., Yu, L., Nussinov, R. and Ma, B. (2014) Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. Int J Mol Sci, 15, 13275-13298.
75. Hwang, S.Y., Zhang, M., Zhang, C., Ma, B., Zheng, J. and Peng, Z. (2014) Carbon monoxide in controlling the surface formation of Group VIII metal nanoparticles. Chem Commun (Camb), 50, 14013-14016.
76. Dai, D., Huang, Q., Nussinov, R. and Ma, B. (2014) Promiscuous and specific recognition among ephrins and Eph receptors. Biochim Biophys Acta, 1844, 1729-1740.
77. Ji, X., Ma, L., Huang, Q., Li, Z., Zhao, J., Huang, W., Ma, B. and Yu, L. (2014) Network Effect of Wt-Mutant P53 Interactions And Implications on P53 Gene Therapy. Current pharmaceutical design, 20, 1259-1267.
78. Luo, Y., Yu, X., Dinkel, P., Zheng, J., Margittai, M., Nussinov, R., Wei, G. and Ma, B. (2013) Molecular Insights into the Reversible Formation of Tau Protein Fibrils. Chemical Communications, 49, 3582-3584.
79. Nussinov, R., Tsai, C.J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu Rev Biophys, 42, 169-189.
80. Luo, Y., Dinkel, P., Yu, X., Margittai, M., Zheng, J., Nussinov, R., Wei, G.H. and Ma, B.Y. (2013) Molecular insights into the reversible formation of tau protein fibrils. Chem. Commun., 49, 3582-3584.
81. Nussinov, R., Tsai, C.J. and Ma, B.Y. (2013) In Dill, K. A. (ed.), Annual Review of Biophysics, Vol 42. Annual Reviews, Palo Alto, Vol. 42, pp. 169-189.
82. Nussinov, R., Ma, B., Tsai, C.J. and Csermely, P. (2013) Allosteric conformational barcodes direct signaling in the cell. Structure, 21, 1509-1521.
83. Xu, Y., Wang, H., Nussinov, R. and Ma, B. (2013) Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics.
84. Yu, X., Luo, Y., Dinkel, P., Zheng, J., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2012) Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem, 287, 14950-14959.
85. Xu, Y., Ma, B. and Nussinov, R. (2012) Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP. J Phys Chem B, 16, 4801-4811.
86. Stagno, J.R., Ma, B., Li, J., Altieri, A.S., Byrd, R.A. and Ji, X. (2012) Crystal structure of a plectonemic RNA supercoil. Nat Commun, 3, 901.
87. Siddiqua, A., Luo, Y., Meyer, V., Swanson, M.A., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R. et al. (2012) Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau. J Am Chem Soc, 134, 10271-10278.
88. Nussinov, R. and Ma, B. (2012) Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol, 10, 2.
89. Hu, L., Cui, W., He, Z., Shi, X., Feng, K., Ma, B. and Cai, Y.D. (2012) Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One, 7, e39369.
90. Ma, B. and Nussinov, R. (2012) Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol, 421, 172-184.
91. Ma, B. and Nussinov, R. (2011) Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide. J Biol Chem, 286, 34244-34253.
92. Ma, B., Tsai, C.J., Haliloglu, T. and Nussinov, R. (2011) Dynamic allostery: linkers are not merely flexible. Structure, 19, 907-917.
93. Miller, Y., Ma, B. and Nussinov, R. (2011) Synergistic interactions between repeats in tau protein and Abeta amyloids may be responsible for accelerated aggregation via polymorphic states. Biochemistry, 50, 5172-5181.
94. Yuan, P., Liang, K., Ma, B., Zheng, N., Nussinov, R. and Huang, J. (2011) Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment. Chem Biol Drug Des, 78, 137-149.
95. Parthasarathy, S., Long, F., Miller, Y., Xiao, Y., McElheny, D., Thurber, K., Ma, B., Nussinov, R. and Ishii, Y. (2011) Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's beta by solid-state NMR spectroscopy. J Am Chem Soc, 133, 3390-3400.
96. Miller, Y., Ma, B. and Nussinov, R. (2011) The unique Alzheimer's beta-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. J Am Chem Soc, 133, 2742-2748.
97. Ma, B. and Nussinov, R. (2010) Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer. J Biol Chem, 285, 37102-37110.
98. Ma, B. and Nussinov, R. (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol, 14, 652-659.
99. Ma, B., Tsai, C.J., Pan, Y. and Nussinov, R. (2010) Why does binding of proteins to DNA or proteins to proteins not necessarily spell function? ACS Chem Biol, 5, 265-272.
100. Miller, Y., Ma, B. and Nussinov, R. (2010) Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A, 107, 9490-9495.
101. Miller, Y., Ma, B. and Nussinov, R. (2010) Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev, 110, 4820-4838.
102. Miller, Y., Ma, B., Tsai, C.J. and Nussinov, R. (2010) Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH. Proc Natl Acad Sci U S A, 107, 14128-14133.
103. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet, 26, 75-83.
104. Yu, X., Wang, Q., Yang, J.C., Buch, I., Tsai, C.J., Ma, B., Cheng, S.Z., Nussinov, R. and Zheng, J. (2009) Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain. Biomacromolecules, 10, 390-399.
105. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control. Phys Biol, 6, 013001.
106. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci, 34, 594-600.
107. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2009) How do transcription factors select specific binding sites in the genome? Nat Struct Mol Biol, 16, 1118-1120.
108. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci.
109. Miller, Y., Ma, B. and Nussinov, R. (2009) Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J, 97, 1168-1177.
110. Ma, B. and Nussinov, R. (2009) Regulating highly dynamic unstructured proteins and their coding mRNAs. Genome Biol, 10, 204.
111. Ma, B. and Nussinov, R. (2009) Amplification of signaling via cellular allosteric relay and protein disorder. Proc Natl Acad Sci U S A, 106, 6887-6888.
112. del Sol, A., Tsai, C.J., Ma, B. and Nussinov, R. (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure, 17, 1042-1050.
113. Zheng, J., Ma, B., Chang, Y. and Nussinov, R. (2008) Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association. Front Biosci, 13, 3919-3930.
114. Zheng, J., Jang, H., Ma, B. and Nussinov, R. (2008) Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B, 112, 6856-6865.
115. Jang, H., Ma, B., Lal, R. and Nussinov, R. (2008) Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J, 95, 4631-4642.
116. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2008) Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem Rev, 108, 1225-1244.
117. Ma, B. and Levine, A.J. (2007) Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Res, 35, 7733-7747.
118. Ma, B., Pan, Y., Zheng, J., Levine, A.J. and Nussinov, R. (2007) Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res, 35, 2986-3001.
119. Zheng, J., Jang, H., Ma, B., Tsai, C.J. and Nussinov, R. (2007) Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J, 93, 3046-3057.
120. Ma, B. and Nussinov, R. (2007) Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr Top Med Chem, 7, 999-1005.
121. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2007) Towards drugs targeting multiple proteins in a systems biology approach. Curr Top Med Chem, 7, 943-951.
122. Jang, H., Ma, B. and Nussinov, R. (2007) Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. BMC Struct Biol, 7, 21.
123. Hu, Z., Bowen, D., Southerland, W.M., del Sol, A., Pan, Y., Nussinov, R. and Ma, B. (2007) Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol, 3, e117.
124. Liu, J., Pan, Y., Ma, B. and Nussinov, R. (2006) "Similarity Trap" in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains. Structure, 14, 1811-1821.
125. Zheng, J., Ma, B. and Nussinov, R. (2006) Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Phys Biol, 3, P1-4.
126. Ma, B. and Nussinov, R. (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol.
127. Jang, H., Ma, B., Woolf, T.B. and Nussinov, R. (2006) Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J, 91, 2848-2859.
128. Zheng, J., Ma, B., Tsai, C.J. and Nussinov, R. (2006) Structural Stability and Dynamics of an Amyloid-forming Peptide GNNQQNY from the Yeast Prion Sup-35. Biophys J.
129. Pan, Y., Ma, B., Levine, A.J. and Nussinov, R. (2006) Comparison of the human and worm p53 structures suggests a way for enhancing stability. Biochemistry, 45, 3925-3933.
130. Ro, D.K., Paradise, E.M., Ouellet, M., Fisher, K.J., Newman, K.L., Ndungu, J.M., Ho, K.A., Eachus, R.A., Ham, T.S., Kirby, J. et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 440, 940-943.
131. Wolfson, H.J., Shatsky, M., Schneidman-Duhovny, D., Dror, O., Shulman-Peleg, A., Ma, B. and Nussinov, R. (2005) From structure to function: methods and applications. Curr Protein Pept Sci, 6, 171-183.
132. Pan, Y., Ma, B. and Nussinov, R. (2005) CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible. J Mol Biol, 350, 514-527.
133. Ma, B., Pan, Y., Gunasekaran, K., Keskin, O., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins. Phys Biol, 2, S56-66.
134. Keskin, O., Ma, B., Rogale, K., Gunasekaran, K. and Nussinov, R. (2005) Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol, 2, S24-S35.
135. Ma, B., Pan, Y., Gunasekaran, K., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface. Proc Natl Acad Sci U S A, 102, 3988-3993.
136. Pan, Y., Ma, B., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) In the Quest for Stable Rescuing Mutants of p53: Computational Mutagenesis of Flexible Loop L1. Biochemistry, 44, 1423-1432.
137. Haspel, N., Zanuy, D., Ma, B., Wolfson, H. and Nussinov, R. (2005) A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. J Mol Biol, 345, 1213-1227.
138. Keskin, O., Ma, B. and Nussinov, R. (2005) Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol, 345, 1281-1294.
139. Haliloglu, T., Keskin, O., Ma, B. and Nussinov, R. (2005) How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J, 88, 1552-1559.
140. Ma, B. and Nussinov, R. (2004) From computational quantum chemistry to computational biology: Experiments and computations are (full) partners. Physical Biology, 1, p23-p26.
141. Li, X., Keskin, O., Ma, B., Nussinov, R. and Liang, J. (2004) Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking. J Mol Biol, 344, 781-795.
142. Zanuy, D., Nurit, H., Tsai, H.H., B., M., Gunasekaran, K., Wolfson, H. and Nussinov, R. (2004) Side chain interactions determine the amyloid organization: a single layer ß-sheet molecular structure of the calcitonin peptide segment 15–19. Physical Biology, 1, 89-99.
143. Tsai, H.H., Zanuy, D., Haspel, N., Gunasekaran, K., Ma, B., Tsai, C.J. and Nussinov, R. (2004) The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Biophys J, 87, 146-158.
144. Tsai, H.H., Tsai, C.J., Ma, B. and Nussinov, R. (2004) In silico protein design by combinatorial assembly of protein building blocks. Protein Sci, 13, 2753-2765.
145. Pan, Y., Ma, B., Keskin, O. and Nussinov, R. (2004) Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem, 279, 30523-30530.
146. Ma, B. and Nussinov, R. (2004) Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. J Biol Chem, 279, 53875-53885.
147. Zanuy, D., Gunasekaran, K., Ma, B., Tsai, H.H., Tsai, C.J. and Nussinov, R. (2004) Insights into amyloid structural formation and assembly through computational approaches. Amyloid, 11, 143-161.
148. Gunasekaran, K., Ma, B. and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins, 57, 433-443.
149. Zanuy, D., Ma, B. and Nussinov, R. (2003) Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J, 84, 1884-1894.
150. Ma, B., Elkayam, T., Wolfson, H. and Nussinov, R. (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A, 100, 5772-5777.
151. Ma, B. and Nussinov, R. (2003) Energy landscape and dynamics of the b-hairpin G peptide and its isomers: Topology and sequences. Protein Sci, 12, 1882-1893.
152. Ma, B. and Nussinov, R. (2003) Molecular dynamics simulations of the unfolding of b2-microglobulin and its variants. Protein Eng, 16, 561-575.
153. Li, W., Ma, B. and Shapiro, B.A. (2003) Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations. Nucleic Acids Research, 31, 629-638.
154. Gunasekaran, K., Ma, B., Ramakrishnan, B., Qasba, P.K. and Nussinov, R. (2003) Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I. Biochemistry, 42, 3674-3687.
155. Gunasekaran, K., Ma, B. and Nussinov, R. (2003) Triggering loops and enzyme function: identification of loops that trigger and modulate movements. J Mol Biol, 332, 143-159.
156. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2002) Thermal unfolding molecular dynamics simulation of E-coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway. Proteins, 46, 308-320.
157. Ma, B., Shatsky, M., Wolfson, H.J. and Nussinov, R. (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci, 11, 184-197.
158. Ma, B. and Nussinov, R. (2002) Molecular dynamics simulations of alanine rich b-sheet oligomers: Insight into amyloid formation. Protein Sci, 11, 2335-2350.
159. Ma, B. and Nussinov, R. (2002) Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Ab16-22, Ab16-35, and Ab10-35): Sequence effects. Proc Natl Acad Sci U S A, 99, 14126-14131.
160. Halperin, I., Ma, B., Wolfson, H. and Nussinov, R. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
161. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S., Wolfson, H. and Nussinov, R. (2001) A hierarchical, building blocks based computational method for protein structure prediction. IBM Journal of Research and Development, Issue on life Science., 45.
162. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S. and Nussinov, R. (2001) Structured disorder and conformational selection. Proteins, 44, 418-427.
163. Tsai, C.D., Ma, B., Kumar, S., Wolfson, H. and Nussinov, R. (2001) Protein folding: binding of conformationally fluctuating building blocks via population selection. Crit Rev Biochem Mol Biol, 36, 399-433.
164. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2001) Molecular dynamics simulation of E-coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations. Protein Sci, 10, 135-148.
165. Ma, B., Wolfson, H.J. and Nussinov, R. (2001) Protein functional epitopes: hot spots, dynamics and combinatorial libraries. Curr Opin Struct Biol, 11, 364-369.
166. Li, W., Ma, B. and Shapiro, B.A. (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. Journal of Biomolecular Structure & Dynamics, 19, 381-396.
167. Nussinov, R., Ma, B. and Wolfson, H. (2000) Computational methods for docking and drug design:functional epitopes and combinatorial libraries. In Current topics in computational Biology. Ed. T. Jiang, T. Smith, Y. Xu and M.Q. Zhang. MIT Press, Boston, MA.
168. Ma, B., Kumar, S., Tsai, C.J., Wolfson, H., Sinha, N. and Nussinov, R. (2000) Protein-ligand interaction: induced fit? Encyclopedia in life science, London, Macmillan Reference Limited.
169. Ma, B., Lii, J.H. and Allinger, N.L. (2000) Molecular polarizabilities and induced dipole moments in molecular mechanics. Journal of Computational Chemistry, 21, 813-825.
170. Ma, B. and Nussinov, R. (2000) Molecular dynamics simulations of a b-hairpin fragment of protein G: balance between side-chain and backbone forces. J Mol Biol, 296, 1091-1104.
171. Ma, B., Kumar, S., Tsai, C.J., Hu, Z. and Nussinov, R. (2000) Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? J Theor Biol, 203, 383-397.
172. Ma, B., Tsai, C.J. and Nussinov, R. (2000) A systematic study of the vibrational free energies of polypeptides in folded and random states. Biophys J, 79, 2739-2753.
173. Ma, B., Tsai, C.J. and Nussinov, R. (2000) Binding and folding: in search of intramolecular chaperone-like building block fragments. Protein Eng, 13, 617-627.
174. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Contribution of Salt Bridges Toward Protein Thermostability. J. Biomol. Struc. and Dynamics, conversation 11, 79-85.
175. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins, 38, 368-383.
176. Kumar, S., Ma, B., Tsai, C.J., Sinha, N. and Nussinov, R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci, 9, 10-19.
177. Hu, Z., Ma, B., Wolfson, H. and Nussinov, R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
178. Buyong, Xiong, J., Lubkowski, J. and Nussinov, R. (2000) Homology modeling and molecular dynamics simulations of lymphotactin. Protein Sci, 9, 2192-2199.
179. Tsai, C.J., Kumar, S., Ma, B. and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function. Protein Sci, 8, 1181-1190.
180. Tsai, C.J., Ma, B. and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci U S A, 96, 9970-9972.
181. Ma, B. and Nussinov, R. (1999) Explicit and implicit water simulations of a b-hairpin peptide. Proteins, 37, 73-87.
182. Ma, B., Kumar, S., Tsai, C.J. and Nussinov, R. (1999) Folding funnels and binding mechanisms. Protein Eng, 12, 713-720.
183. Lii, J.H., Ma, B. and Allinger, N.L. (1999) Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Computational Chemistry, 20, 1593-1603.
184. Kumar, S., Ma, B., Tsai, C.J., Wolfson, H. and Nussinov, R. (1999) Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys, 31, 141-164.
185. Ma, B., Schaefer, H.F. and Allinger, N.L. (1998) Theoretical studies of the potential energy surfaces and compositions of the D-aldo- and D-ketohexoses. Journal of the American Chemical Society, 120, 3411-3422.
186. Kirschner, K., Ma, B., Bowen, J. and Duncan, M. (1998) Theoretical investigation of the Ca+N-2 and Ca2+N-2 complexes. CHEMICAL PHYSICS LETTERS, 295, 204-210.
187. King, R.A., Allen, W.D., Ma, B. and Schaefer, H.F. (1998) Fragmentation surface of triplet ketene. Faraday Discussions, 23-50.
188. Ma, B., Schaefer, H.F. and Allinger, N.L. (1997) Computational Studies of Structures and Reactions of Phosphate derivatives. in Recent Research Development in Chemical Science, Transworld Research Network, 1.37.
189. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1997) A molecular mechanics study of the cholesteryl acetate crystal: Evaluation of interconversion among rg, rz, and ra bond lengths. Journal of the American Chemical Society, 119, 2570-2573.
190. Ma, B. and Allinger, N.L. (1997) Calculation of rz structures from rs structures. Journal of Molecular Structure, 413, 395-404.
191. Ma, B., Collins, C.L. and Schaefer, H.F. (1996) Periodic trends for transition metal dihydrides MH2, dihydride dihydrogen complexes MH2* H-2, and tetrahydrides MH4 (M=Ti,V, and Cr). Journal of the American Chemical Society, 118, 870-879.
192. Ma, B., Lii, J.H., Schaefer, H.F. and Allinger, N.L. (1996) Systematic comparison of experimental, quantum mechanical, and molecular mechanical bond lengths for organic molecules. Journal of Physical Chemistry, 100, 8763-8769.
193. Ma, B. and Schaefer, H.F. (1996) Singlet-triplet energy separation and barrier for ring closure for trimethylenemethane and its complexes. Chemical Physics, 207, 31-41.
194. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1996) Quantum mechanical and molecular mechanics (MM3) studies of hydrazines. Journal of Physical Chemistry, 100, 11297-11304.
195. Ma, B., Allinger, N.L. and Schaefer, H.F. (1996) Spectroscopic constants and potential energy surfaces for silanone (H2SiO), hydroxysilylene (HSiOH), the hydroxysilylene dimer, and the disilynyl radical (Si2H). Journal of Chemical Physics, 105, 5731-5736.
196. Goldstein, E., Ma, B., Lii, J.H. and Allinger, N.L. (1996) Molecular mechanics calculations (MM3) on nitriles and alkynes. Journal of Physical Organic Chemistry, 9, 191-202.
197. Ma, B., Yamaguchi, Y. and Schaefer, H.F. (1995) Spectroscopic constants and potential energy surfaces for the possible interstellar molecules AlNC and AlCN. Molecular Physics, 86, 1331-1337.
198. Ma, B., Meredith, C. and Schaefer, H.F. (1995) The Quest for a Metaphosphate Intermediate - the Mechanisms for Hydrolysis of Pyrophosphates with and without Catalysis. Journal of Physical Chemistry, 99, 3815-3822.
199. Ma, B., Sulzbach, H.M., Remington, R.B. and Schaefer, H.F. (1995) Structure, Strain-Energy, and Magnetic-Susceptibility of 4-Paracyclophane and the Activation-Energy for Its Interconversion with 1,4-Tetramethylene Dewar Benzene. Journal of the American Chemical Society, 117, 8392-8400.
200. Hu, C.H., Ma, B. and Schaefer, H.F. (1995) The Synchronous Thermal-Decomposition Mechanism of Azoisopropane. Molecular Physics, 85, 769-779.
201. Souter, P.F., Andrews, L., Downs, A.J., Greene, T.M., Ma, B. and Schaefer, H.F. (1994) Observed and Calculated Raman-Spectra of the Ga2H6 and Ga2D6 Molecules. Journal of Physical Chemistry, 98, 12824-12827.
202. Ma, B. and Schaefer, H.F. (1994) Singlet Methylcarbene - Equilibrium Geometry or Transition-State. Journal of the American Chemical Society, 116, 3539-3542.
203. Ma, B., Sulzbach, H.M., Xie, Y.M. and Schaefer, H.F. (1994) p-Electron Delocalization and Compression in Acyclic Acetylenic Precursors to Multidimensional Carbon Networks - Comparison with Experiment for the Recently Synthesized Tris(Trimethylsilyl)-Substituted Tetraethynylmethane - Structures, Thermochemistry, Infrared-Spectra, Polarizabilities, and Hyperpolarizabilities. Journal of the American Chemical Society, 116, 3529-3538.
204. Ma, B. and Schaefer, H.F. (1994) Toward the Observation of Silanone (H2SiO) and Hydroxysilylene (HSiOH) Via Microwave Spectroscopy. Journal of Chemical Physics, 101, 2734-2739.
205. Ma, B., Meredith, C. and Schaefer, H.F. (1994) Pyrophosphate Structures and Reactions - Evaluation of Electrostatic Effects on the Pyrophosphates with and without Alkali Cations. Journal of Physical Chemistry, 98, 8216-8223.
206. Ma, B., Xie, Y.M., Shen, M.Z. and Schaefer, H.F. (1993) PO3-.(H2O)N Clusters - Molecular Anion Structures, Energetics, and Vibrational Frequencies. Journal of the American Chemical Society, 115, 1943-1951.
207. Ma, B., Xie, Y.M., Shen, M.Z., Schleyer, P.V. and Schaefer, H.F. (1993) Isomerization of PO3-*(H2O)N Clusters to H2PO4-*(H2O)N-1 - Transition-States and Barrier Heights. Journal of the American Chemical Society, 115, 11169-11179.
208. Ma, B., Xie, Y.M. and Schaefer, H.F. (1992) Tetraethynylethylene, a Molecule with 4 Very Short C-C Single Bonds - Interpretation of the Infrared-Spectrum. Chemical Physics Letters, 191, 521-526.
209. Ma, B. and Xie, H. (1991) Review of Sulfonated EPDM Ionomer Elastomer. Hecheng Xiangjiao Gongye (J. of Synthetic Rubber Industry, chinese), 14, 227.
210. Ma, B. and Xie, H. (1990) Preparation of Sulfonated EPDM Ionomer with Phase Transfer Catalyst. Hecheng Xiangjiao Gongye (J. of Synthetic Rubber Industry, chinese), 13, 183.
211. Xie, H. and Ma, B. (1989) Blends of Sulfonated EPDM Ionomers with Several Kinds of Polymers. in Contemp Top. Polym. Sci. Ed. Culbertson, B. M., B28, 51.
212. Xie, H.Q. and Ma, B. (1989) Properties of Sulfonated EPDM Ionomers Obtained by Sulfonation in the Presence of Phase-Transfer Catalyst. Journal of Macromolecular Science-Physics, B28, 51-67.
213. Zuo, G., Xia, L., Ma, B. and Wang, Y. (1988) Reinforced Composites Containing Asbestos Fiber. I. Surface Treatment Efficiency of the Asbestos Fiber. Gaofenzi Cailiao Kexue Yu Gongchen ( polymer material science and technology, chinese), 4, 601.


2020-至今： 英国上市公司官网365，教授
2003-2020： 美国Frederick国家癌症研究实验室， 美国国家癌症研究所 ，资深科学家。
2002-2003： 美国Locus Pharmaceuticals, Inc; Philadelphia, 研究员。
1998-2002： 美国国家癌症研究所研究员。
1995-1998： 美国 佐治亚大学， 化学系 N. L. Allinger 研究组，博士后。
1991-1995： 美国 佐治亚大学，化学系,计算量子化学中心（CCQC）, 物理化学专业， 博士。
1987-1991： 湖北化学研究所， 助理研究员。
1984-1987： 湖北化学研究所， 高分子化学专业， 硕士。
1980-1984： 合肥工业大学，化学工程系， 高分子化学工程专业， 学士。

英国上市公司官网365马步勇课题组招聘博士后(分子生物学实验一名，计算方向不限）
研究方向
1. 分子模拟结合人工智能在物理生物及抗体药物设计中的应用。
2. 生物大分子的动态结构与性能以及免疫系统的信号传导。
3. 多功能计算机辅助药物设计平台研发。
4. (实验）抗体及蛋白质工程。

招聘条件
1. 在国内外知名高校及研究机构获得博士学位，分子生物学，生物物理，计算物理、计算化学、计算生物学，计算机科学等相关专业；
2. 熟悉常用的计算化学和计算生物学通用程序，熟练建立机器学习和深度学习模型和软件系统开发；实验方向：熟练的抗体及蛋白质工程技能。
3. 在生物大分子结构与性能方面有深入的了解；
4. 良好的科研论文的写作能力和发表记录；
5. 具有良好的创新意识和团队合作精神，具有良好的交流沟通能力。

岗位待遇
按照英国上市公司官网365有关政策执行 。

1. 基于高性能计算和人工智能推动新型生物药物设计与优化，涵盖多肽和抗体药物，药用和工业用生物酶，以及小分子/多肽/融合蛋白。
2. 蛋白质凝聚疾病，特别是神经退行疾病的分子机理及药物开发。
3. 计算生物学/ 计算免疫学的基础研究方面，致力于探讨生物大分子的动态结构与性能以及免疫系统的信号传导。
4. 医用/药用材料基因组。


英国上市公司官网365马步勇课题组招聘博士后(分子生物学实验一名，计算方向不限）
研究方向
1. 分子模拟结合人工智能在物理生物及抗体药物设计中的应用。
2. 生物大分子的动态结构与性能以及免疫系统的信号传导。
3. 多功能计算机辅助药物设计平台研发。
4. (实验）抗体及蛋白质工程。

招聘条件
1. 在国内外知名高校及研究机构获得博士学位，分子生物学，生物物理，计算物理、计算化学、计算生物学，计算机科学等相关专业；
2. 熟悉常用的计算化学和计算生物学通用程序，熟练建立机器学习和深度学习模型和软件系统开发；实验方向：熟练的抗体及蛋白质工程技能。
3. 在生物大分子结构与性能方面有深入的了解；
4. 良好的科研论文的写作能力和发表记录；
5. 具有良好的创新意识和团队合作精神，具有良好的交流沟通能力。

岗位待遇
按照英国上市公司官网365有关政策执行 。

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自然指数期刊论文： 43 篇


2023
1. Ding, J., Lee, Y.T., Bhandari, Y., Schwieters, C.D., Fan, L., Yu, P., Tarosov, S.G., Stagno, J.R., Ma, B., Nussinov, R. et al. (2023) Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun, 14, 714.

2022
2. Tsuji, K., Hymel, D., Ma, B., Tamamura, H., Nussinov, R. and Burke, T.R., Jr. Development of ultra-high affinity bivalent ligands targeting the polo-like kinase 1. RSC Chem Biol, 2022， 3, 1111-1120.
3. Kabir, K.L., Ma, B., Nussinov, R. and Shehu, A. Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody. Biomolecules, 2022， 12.
4. Song NY, Li X, Ma B, Willette-Brown J, Zhu F, Jiang C, et al. IKKalpha-deficient lung adenocarcinomas generate an immunosuppressive microenvironment by overproducing Treg-inducing cytokines. Proc Natl Acad Sci U S A. 2022;119.

2021
5. Bai G, Ge Y, Su Y, Chen S, Zeng X, Lu H, et al. Computational Construction of a Single-Chain Bi-Paratopic Antibody Allosterically Inhibiting TCR-Staphylococcal Enterotoxin B Binding. Front Immunol. 2021;12:732938
6. Ma B, Bai G, Nussinov R, Ding J, Wang YX. Conformational Ensemble of TteAdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition. The journal of physical chemistry B. 2021;125:2589-96.
7. Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesne S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev. 2021;121:2545-647.
8. Lucchesi CA, Zhang J, Ma B, Nussinov R, Chen X. Survivin Expression is Differentially Regulated by a Selective Crosstalk between Rbm38 and miRNAs let-7b or miR-203a. Cancer Res. 2021 doi: 10.1158/0008-5472.
9. Zhao, J.; Mohan, N.; Nussinov, R.; Ma, B.; Wu, W.J. Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers. Antibodies 2021, 10, 7. https://doi.org/10.3390/antib10010007
10. Zhao J, Nussinov R, Ma B. The Allosteric Effect in Antibody-Antigen Recognition. Methods Mol Biol. 2021; 2253:175-183. doi: 10.1007/978-1-0716-1154-8_11.
2020
11. Chen, Y. Zhao, J. Nussinov, R. Wei, G. Ma, B. Computational Investigation of Gantenerumab and Crenerzumab’s Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue， ACS Chem Neurosci, 11(20):3233-3244.
12. He, Y, Agnihotri, P. Rangarajan,S. Chen, Y. Kerzic, M. Ma, B. Nussinov, R. Mariuzza, R. and Orban, J. Peptide–MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs), J. Mol. Bio. 432(24):166697.
2019
13. Luo, H. Hu, L. Ma, B. Zhao, M. Luo, M. Deng, M. Deng, S. Ye, H. Lin, T. Chen, J. Lu, H. Molecular dynamics based improvement of the solubilizing self-cleavable tag Zbasic-ΔI-CM application in the preparation of recombinant proteins in Escherichia coli. Biochemical and biophysical research communications 513 (2), 412-418
14. Lucchesi, C.A., Zhang, J., Ma, B., Chen, M. and Chen, X. Disruption of the Rbm38-eIF4E complex with a synthetic peptide Pep8 increases p53 expression. Cancer Res. 2019 79(4): 807–818.
15. Lei, J., Qi, R., Tang, Y., Wang, W., Wei, G., Nussinov, R. and Ma, B. Conformational stability and dynamics of the cancer-associated isoform Delta133p53beta are modulated by p53 peptides and p53-specific DNA. FASEB J 2019, 33(3): 4225–4235.
16. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2019) Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods Mol Biol, 1851, 317-335.
17. Guven-Maiorov, E. Tsai, CJ. Ma, B. Nussinov, R. Interface-based structural prediction of novel host-pathogen interactions. Computational Methods in Protein Evolution, 2019, 317-335
18. Zhao, J., Nussinov, R. and Ma, B. Antigen binding allosterically promotes Fc receptor recognition. MAbs, 11 (1), 58-74
2018
19. Zhao, J., Zhang, B., Zhu, J., Nussinov, R. and Ma, B. (2018) Structure and energetic basis of overrepresented lambda light chain in systemic light chain amyloidosis patients. BBA Molecular Basis of Desease. doi: 10.1016/j.bbadis.2017.12.009. 1864, 2294-2303
20. Zhang, M. Zheng, J. Nussinov, R. Ma, B. Molecular recognition between Aβ-specific single-domain antibody and Aβ Misfolded aggregates. Antibodies 7 (3), 25
21. Li, X., Dong, X., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2018) The distinct structural preferences of tau protein repeat domains. Chem Commun (Camb), 54, 5700-5703.
22. Weismiller, H.A., Murphy, R., Wei, G., Ma, B., Nussinov, R. and Margittai, M. (2018) Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms. J Biol Chem, 293, 17336-17348.
23. Rangarajan, S., He, Y., Chen, Y., Kerzic, M.C., Ma, B., Gowthaman, R., Pierce, B.G., Nussinov, R., Mariuzza, R.A. and Orban, J. (2018) Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. J Biol Chem, 293, 15991-16005.
24. Qi, R., Wei, G., Ma, B. and Nussinov, R. (2018) Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example. Methods Mol Biol, 1777, 101-119.
25. Ren, B., Hu, R., Zhang, M., Liu, Y., Xu, L., Jiang, B., Ma, J., Ma, B., Nussinov, R. and Zheng, J. (2018) Experimental and Computational Protocols for Studies of Cross-Seeding Amyloid Assemblies. Methods Mol Biol, 1777, 429-447.
26. Song, N.Y., Zhu, F., Wang, Z., Willette-Brown, J., Xi, S., Sun, Z., Su, L., Wu, X., Ma, B., Nussinov, R. et al. (2018) IKKalpha inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways. Proc Natl Acad Sci U S A, 115, E812-E821.
27. Qian, Z., Zou, Y., Zhang, Q., Chen, P., Ma, B., Wei, G. and Nussinov, R. (2018) Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition. Biochim Biophys Acta. s0005-2736, 30046-30044.
28. J Zhao, R Nussinov, WJ Wu, B Ma In silico methods in antibody design Antibodies 7 (3), 22
2017
29. Wang, M., Zhu, D., Zhu, J., Nussinov, R. and Ma, B. (2017) Local and global anatomy of antibody-protein antigen recognition. J Mol Recognit. 21, e2693.
30. Zhao, J., Nussinov, R. and Ma, B. (2017) Mechanisms of recognition of Abeta monomer, oligomer, and fibril by homologous antibodies. J Biol Chem, 292, 18325-18343.
31. Dong, X., Sun, Y., Wei, G., Nussinov, R. and Ma, B.* (2017) Binding of protofibrillar Aß trimers to lipid bilayer surface enhances Aß structural stability and causes membrane thinning Phys Chem Chem Phys. 19, 27556-27569.
32. Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. (2017) Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer. J Mol Biol, 429, 3925-3941.
33. Libardo, M.D.J., Bahar, A.A., Ma, B., Fu, R., McCormick, L.E., Zhao, J., McCallum, S.A., Nussinov, R., Ren, D., Angeles-Boza, A.M. et al. (2017) Nuclease Activity Gives an Edge to Host-Defense Peptide Piscidin 3 over Piscidin 1, Rendering it more Effective against Persisters and Biofilms. FEBS J. 284 (21), 3662-3683
34. Zhang, M., Zheng, J., Nussinov, R. and Ma, B. (2017) Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane. Sci Rep, 7, 2635.
35. Xu, L., Ma, B., Nussinov, R. and Thompson, D. (2017) Familial Mutations May Switch Conformational Preferences in alpha-Synuclein Fibrils. ACS Chem Neurosci, 8, 837-849.
36. Zhao, J., Nussinov, R. and Ma, B. (2017) Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains. Protein Eng Des Sel, 30, 67-76.
37. Gong, Y., Zhu, Y., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2017) Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity. J Phys Chem B, 121, 508-517.
38. Gan, W., Schneidman, D., Zhang, N., Ma, B. and Nussinov, R. (2017) Probing Oligomerized Conformations of Defensin in the Membrane. Methods Mol Biol, 1529, 353-362.
2016
39. Zou, Y., Sun, Y., Zhu, Y., Ma, B., Nussinov, R. and Zhang, Q. (2016) Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci, 7, 286-296.
40. 166. Zhu, Y., Ma, B., Qi, R., Nussinov, R. and Zhang, Q. (2016) Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations. J Phys Chem B, 120, 3551-3559.
41. Zhan, C., Qi, R., Wei, G., Guven-Maiorov, E., Nussinov, R. and Ma, B. (2016) Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization. Protein Eng Des Sel, 29, 347-354.
42. Maximova, T., Moffatt, R., Ma, B., Nussinov, R. and Shehu, A. (2016) Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol, 12, e1004619.
43. Ma, B., Zhao, J. and Nussinov, R. (2016) Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. Biochim Biophys Acta, 1860, 2672-2681.
44. Ma, B. and Nussinov, R. (2016) Protein dynamics: Conformational footprints. Nat Chem Biol, 12, 890-891.
45. Lei, J., Qi, R., Wei, G., Nussinov, R. and Ma, B. (2016) Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Phys Chem Chem Phys, 18, 8098-8107.
46. Hewitt, W.M., Lountos, G.T., Zlotkowski, K., Dahlhauser, S.D., Saunders, L.B., Needle, D., Tropea, J.E., Zhan, C., Wei, G., Ma, B. et al. (2016) Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Angew Chem Int Ed Engl, 55, 5703-5707.
47. Xu, L., Nussinov, R. and Ma, B. (2016) Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the alpha-synuclein fibrils. Eur J Med Chem, 121, 841-850.
48. Xu, L., Zheng, J., Margittai, M., Nussinov, R. and Ma, B. (2016) How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability? ACS Chem Neurosci, 7, 565-575.
49. Xu, L., Nussinov, R. and Ma, B. (2016) Allosteric stabilization of the amyloid-beta peptide hairpin by the fluctuating N-terminal. Chem Commun (Camb), 52, 1733-1736.
50. Wei, G., Xi, W., Nussinov, R. and Ma, B. (2016) Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev, 116, 6516-6551.
2015
51. Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R. and Ishii, Y. (2015) Abeta(1-42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease. Nat Struct Mol Biol, 22, 499-505.
52. Qi, R., Luo, Y., Wei, G., Nussinov, R. and Ma, B. (2015) Aβ “Stretching-and-Packing” Cross-Seeding Mechanism Can Trigger Tau Protein Aggregation. The Journal of Physical Chemistry Letters, 6, 3276-3282.
53. Zhu, Y., Yang, S., Qi, R., Zou, Y., Ma, B., Nussinov, R. and Zhang, Q. (2015) Effects of the C-Terminal Tail on the Conformational Dynamics of Human Neuronal Calcium Sensor-1 Protein. J Phys Chem B, 119, 14236-14244.
54. Datta, S.A., Clark, P.K., Fan, L., Ma, B., Harvin, D.P., Sowder, R.C., 2nd, Nussinov, R., Wang, Y.X. and Rein, A. (2015) Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly. J Virol, 90, 1773-1787.
55. Clausen, R., Ma, B., Nussinov, R. and Shehu, A. (2015) Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PLoS Comput Biol, 11, e1004470.
56. Baram, M., Atsmon-Raz, Y., Ma, B., Nussinov, R. and Miller, Y. (2015) Amylin-Abeta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. Phys Chem Chem Phys. 18(4): 2330–2338.
57. Xu, L., Shan, S., Chen, Y., Wang, X., Nussinov, R. and Ma, B. (2015) Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Abeta40 Peptide Oligomerization. J Chem Inf Model, 55, 1218-1230.
58. Zhou, P., Zhang, N., Nussinov, R. and Ma, B. (2015) Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. J Comput Biol, 22, 876-886.
59. Fetics, S.K., Guterres, H., Kearney, B.M., Buhrman, G., Ma, B., Nussinov, R. and Mattos, C. (2015) Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD. Structure, 23, 505-516.
60. Miller, Y., Ma, B. and Nussinov, R. (2015) Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity. J Phys Chem B, 119, 482-490.
61. Cronin, M., Coolbaugh, M.J., Nellis, D., Zhu, J., Wood, D.W., Nussinov, R. and Ma, B. (2015) Dynamics differentiate between active and inactive inteins. Eur J Med Chem, 91, 51-62.
2014
62. Zhu, Y., Wu, Y., Luo, Y., Zou, Y., Ma, B. and Zhang, Q. (2014) R102Q mutation shifts the salt-bridge network and reduces the structural flexibility of human neuronal calcium sensor-1 protein. J Phys Chem B, 118, 13112-13122.
63. Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q. and Nussinov, R. (2014) Investigation of the interactions between the EphB2 receptor and SNEW peptide variants. Growth Factors, 32, 236-246.
64. Huang, Q., Yu, L., Levine, A.J., Nussinov, R. and Ma, B. (2014) Dipeptide analysis of p53 mutations and evolution of p53 family proteins. Biochim Biophys Acta, 1844, 198-206.
65. Nussinov, R., Ma, B. and Tsai, C.J. (2014) Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys Chem, 186, 22-30.
66. Ma, B. and Nussinov, R. (2014) Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des, 20, 1293-1301.
67. Qi, R., Luo, Y., Ma, B.*, Nussinov, R. and Wei, G. (2014) Conformational distribution and alpha-helix to beta-sheet transition of human amylin fragment dimer. Biomacromolecules, 15, 122-131.
68. Meyer, V., Dinkel, P.D., Luo, Y., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R., Eaton, S.S. et al. (2014) Single mutations in tau modulate the populations of fibril conformers through seed selection. Angew Chem Int Ed Engl, 53, 1590-1593.
69. Luo, Y., Ma, B., Nussinov, R. and Wei, G. (2014) Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. J Phys Chem Lett, 5, 3026-3031.
70. Ji, X., Huang, Q., Yu, L., Nussinov, R. and Ma, B. (2014) Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. Int J Mol Sci, 15, 13275-13298.
71. Hwang, S.Y., Zhang, M., Zhang, C., Ma, B., Zheng, J. and Peng, Z. (2014) Carbon monoxide in controlling the surface formation of Group VIII metal nanoparticles. Chem Commun (Camb), 50, 14013-14016.
72. Dai, D., Huang, Q., Nussinov, R. and Ma, B. (2014) Promiscuous and specific recognition among ephrins and Eph receptors. Biochim Biophys Acta, 1844, 1729-1740.
73. Ji, X., Ma, L., Huang, Q., Li, Z., Zhao, J., Huang, W., Ma, B. and Yu, L. (2014) Network Effect of Wt-Mutant P53 Interactions And Implications on P53 Gene Therapy. Current pharmaceutical design, 20, 1259-1267.
2013
74. Luo, Y., Yu, X., Dinkel, P., Zheng, J., Margittai, M., Nussinov, R., Wei, G. and Ma, B. (2013) Molecular Insights into the Reversible Formation of Tau Protein Fibrils. Chemical Communications, DOI: 10.1039/c3cc00241a.
75. Nussinov, R., Tsai, C.J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu Rev Biophys, 42, 169-189.
76. Nussinov, R., Ma, B. and Tsai, C.J. (2013) A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. Biochim Biophys Acta, 1834, 820-829.
77. Ma, B. and Nussinov, R. (2013) Structured crowding and its effects on enzyme catalysis. Top Curr Chem, 337, 123-137.
78. Nussinov, R., Ma, B., Tsai, C.J. and Csermely, P. (2013) Allosteric conformational barcodes direct signaling in the cell. Structure, 21, 1509-1521.
79. Xu, Y., Wang, H., Nussinov, R. and Ma, B. (2013) Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome. Proteomics. 13(8):1339-51
80. Yu, X., Luo, Y., Dinkel, P., Zheng, J., Wei, G., Margittai, M., Nussinov, R. and Ma, B. (2012) Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem, 287, 14950-14959.
2012
81. Xu, Y., Ma, B. and Nussinov, R. (2012) Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP. J Phys Chem B, 16, 4801-4811.
82. Stagno, J.R., Ma, B., Li, J., Altieri, A.S., Byrd, R.A. and Ji, X. (2012) Crystal structure of a plectonemic RNA supercoil. Nat Commun, 3, 901.
83. Siddiqua, A., Luo, Y., Meyer, V., Swanson, M.A., Yu, X., Wei, G., Zheng, J., Eaton, G.R., Ma, B., Nussinov, R. et al. (2012) Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau. J Am Chem Soc, 134, 10271-10278.
84. Nussinov, R. and Ma, B. (2012) Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol, 10, 2.
85. Hu, L., Cui, W., He, Z., Shi, X., Feng, K., Ma, B. and Cai, Y.D. (2012) Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One, 7, e39369.
86. Ma, B. and Nussinov, R. (2012) Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol, 421, 172-184.
2011
87. Ma, B. and Nussinov, R. (2011) Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide. J Biol Chem, 286, 34244-34253.
88. Ma, B., Tsai, C.J., Haliloglu, T. and Nussinov, R. (2011) Dynamic allostery: linkers are not merely flexible. Structure, 19, 907-917.
89. Miller, Y., Ma, B. and Nussinov, R. (2011) Synergistic interactions between repeats in tau protein and Abeta amyloids may be responsible for accelerated aggregation via polymorphic states. Biochemistry, 50, 5172-5181.
90. Yuan, P., Liang, K., Ma, B., Zheng, N., Nussinov, R. and Huang, J. (2011) Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment. Chem Biol Drug Des, 78, 137-149.
91. Parthasarathy, S., Long, F., Miller, Y., Xiao, Y., McElheny, D., Thurber, K., Ma, B., Nussinov, R. and Ishii, Y. (2011) Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's beta by solid-state NMR spectroscopy. J Am Chem Soc, 133, 3390-3400.
92. Miller, Y., Ma, B. and Nussinov, R. (2011) The unique Alzheimer's beta-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions. J Am Chem Soc, 133, 2742-2748.
2010
93. Ma, B. and Nussinov, R. (2010) Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer. J Biol Chem, 285, 37102-37110.
94. Ma, B. and Nussinov, R. (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol, 14, 652-659.
95. Ma, B., Tsai, C.J., Pan, Y. and Nussinov, R. (2010) Why does binding of proteins to DNA or proteins to proteins not necessarily spell function? ACS Chem Biol, 5, 265-272.
96. Miller, Y., Ma, B. and Nussinov, R. (2010) Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A, 107, 9490-9495.
97. Miller, Y., Ma, B. and Nussinov, R. (2010) Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev, 110, 4820-4838.
98. Miller, Y., Ma, B., Tsai, C.J. and Nussinov, R. (2010) Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH. Proc Natl Acad Sci U S A, 107, 14128-14133.
99. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet, 26, 75-83.
Before 2010
100. Yu, X., Wang, Q., Yang, J.C., Buch, I., Tsai, C.J., Ma, B., Cheng, S.Z., Nussinov, R. and Zheng, J. (2009) Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain. Biomacromolecules, 10, 390-399.
101. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control. Phys Biol, 6, 013001.
102. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci, 34, 594-600.
103. Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2009) How do transcription factors select specific binding sites in the genome? Nat Struct Mol Biol, 16, 1118-1120.
104. Tsai, C.J., Ma, B. and Nussinov, R. (2009) Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci. 34(12):594-600.
105. Miller, Y., Ma, B. and Nussinov, R. (2009) Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J, 97, 1168-1177.
106. Ma, B. and Nussinov, R. (2009) Regulating highly dynamic unstructured proteins and their coding mRNAs. Genome Biol, 10, 204.
107. Ma, B. and Nussinov, R. (2009) Amplification of signaling via cellular allosteric relay and protein disorder. Proc Natl Acad Sci U S A, 106, 6887-6888.
108. del Sol, A., Tsai, C.J., Ma, B. and Nussinov, R. (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure, 17, 1042-1050.
109. Zheng, J., Ma, B., Chang, Y. and Nussinov, R. (2008) Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association. Front Biosci, 13, 3919-3930.
110. Zheng, J., Jang, H., Ma, B. and Nussinov, R. (2008) Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B, 112, 6856-6865.
111. Jang, H., Ma, B., Lal, R. and Nussinov, R. (2008) Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J, 95, 4631-4642.
112. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2008) Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem Rev, 108, 1225-1244.
113. Ma, B. and Levine, A.J. (2007) Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Res, 35, 7733-7747.
114. Ma, B., Pan, Y., Zheng, J., Levine, A.J. and Nussinov, R. (2007) Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res, 35, 2986-3001.
115. Zheng, J., Jang, H., Ma, B., Tsai, C.J. and Nussinov, R. (2007) Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J, 93, 3046-3057.
116. Ma, B. and Nussinov, R. (2007) Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr Top Med Chem, 7, 999-1005.
117. Keskin, O., Gursoy, A., Ma, B. and Nussinov, R. (2007) Towards drugs targeting multiple proteins in a systems biology approach. Curr Top Med Chem, 7, 943-951.
118. Jang, H., Ma, B. and Nussinov, R. (2007) Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. BMC Struct Biol, 7, 21.
119. Hu, Z., Bowen, D., Southerland, W.M., del Sol, A., Pan, Y., Nussinov, R. and Ma, B. (2007) Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol, 3, e117.
120. Liu, J., Pan, Y., Ma, B. and Nussinov, R. (2006) "Similarity Trap" in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains. Structure, 14, 1811-1821.
121. Zheng, J., Ma, B. and Nussinov, R. (2006) Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Phys Biol, 3, P1-4.
122. Ma, B. and Nussinov, R. (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol.
123. Jang, H., Ma, B., Woolf, T.B. and Nussinov, R. (2006) Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J, 91, 2848-2859.
124. Zheng, J., Ma, B., Tsai, C.J. and Nussinov, R. (2006) Structural Stability and Dynamics of an Amyloid-forming Peptide GNNQQNY from the Yeast Prion Sup-35. Biophys J.
125. Pan, Y., Ma, B., Levine, A.J. and Nussinov, R. (2006) Comparison of the human and worm p53 structures suggests a way for enhancing stability. Biochemistry, 45, 3925-3933.
126. Ma, B. and Nussinov, R. (2006) The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant. Biophys J, 90, 3365-3374.
127. Wolfson, H.J., Shatsky, M., Schneidman-Duhovny, D., Dror, O., Shulman-Peleg, A., Ma, B. and Nussinov, R. (2005) From structure to function: methods and applications. Curr Protein Pept Sci, 6, 171-183.
128. Pan, Y., Ma, B. and Nussinov, R. (2005) CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible. J Mol Biol, 350, 514-527.
129. Ma, B., Pan, Y., Gunasekaran, K., Keskin, O., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins. Phys Biol, 2, S56-66.
130. Keskin, O., Ma, B., Rogale, K., Gunasekaran, K. and Nussinov, R. (2005) Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol, 2, S24-S35.
131. Ma, B., Pan, Y., Gunasekaran, K., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface. Proc Natl Acad Sci U S A, 102, 3988-3993.
132. Pan, Y., Ma, B., Venkataraghavan, R.B., Levine, A.J. and Nussinov, R. (2005) In the Quest for Stable Rescuing Mutants of p53: Computational Mutagenesis of Flexible Loop L1. Biochemistry, 44, 1423-1432.
133. Haspel, N., Zanuy, D., Ma, B., Wolfson, H. and Nussinov, R. (2005) A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. J Mol Biol, 345, 1213-1227.
134. Keskin, O., Ma, B. and Nussinov, R. (2005) Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol, 345, 1281-1294.
135. Haliloglu, T., Keskin, O., Ma, B. and Nussinov, R. (2005) How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J, 88, 1552-1559.
136. Ma, B. and Nussinov, R. (2004) From computational quantum chemistry to computational biology: Experiments and computations are (full) partners. Physical Biology, 1, p23-p26.
137. Li, X., Keskin, O., Ma, B., Nussinov, R. and Liang, J. (2004) Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking. J Mol Biol, 344, 781-795.
138. Zanuy, D., Nurit, H., Tsai, H.H., Ma, B., Gunasekaran, K., Wolfson, H. and Nussinov, R. (2004) Side chain interactions determine the amyloid organization: a single layer ß-sheet molecular structure of the calcitonin peptide segment 15–19. Physical Biology, 1, 89-99.
139. Tsai, H.H., Zanuy, D., Haspel, N., Gunasekaran, K., Ma, B., Tsai, C.J. and Nussinov, R. (2004) The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Biophys J, 87, 146-158.
140. Tsai, H.H., Tsai, C.J., Ma, B. and Nussinov, R. (2004) In silico protein design by combinatorial assembly of protein building blocks. Protein Sci, 13, 2753-2765.
141. Pan, Y., Ma, B., Keskin, O. and Nussinov, R. (2004) Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem, 279, 30523-30530.
142. Ma, B. and Nussinov, R. (2004) Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. J Biol Chem, 279, 53875-53885.
143. Zanuy, D., Gunasekaran, K., Ma, B., Tsai, H.H., Tsai, C.J. and Nussinov, R. (2004) Insights into amyloid structural formation and assembly through computational approaches. Amyloid, 11, 143-161.
144. Gunasekaran, K., Ma, B. and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins, 57, 433-443.
145. Zanuy, D., Ma, B. and Nussinov, R. (2003) Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J, 84, 1884-1894.
146. Ma, B., Elkayam, T., Wolfson, H. and Nussinov, R. (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A, 100, 5772-5777.
147. Ma, B. and Nussinov, R. (2003) Energy landscape and dynamics of the b-hairpin G peptide and its isomers: Topology and sequences. Protein Sci, 12, 1882-1893.
148. Ma, B. and Nussinov, R. (2003) Molecular dynamics simulations of the unfolding of b2-microglobulin and its variants. Protein Eng, 16, 561-575.
149. Li, W., Ma, B. and Shapiro, B.A. (2003) Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations. Nucleic Acids Research, 31, 629-638.
150. Gunasekaran, K., Ma, B., Ramakrishnan, B., Qasba, P.K. and Nussinov, R. (2003) Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I. Biochemistry, 42, 3674-3687.
151. Gunasekaran, K., Ma, B. and Nussinov, R. (2003) Triggering loops and enzyme function: identification of loops that trigger and modulate movements. J Mol Biol, 332, 143-159.
152. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2002) Thermal unfolding molecular dynamics simulation of E-coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway. Proteins, 46, 308-320.
153. Ma, B., Shatsky, M., Wolfson, H.J. and Nussinov, R. (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci, 11, 184-197.
154. Ma, B. and Nussinov, R. (2002) Molecular dynamics simulations of alanine rich b-sheet oligomers: Insight into amyloid formation. Protein Sci, 11, 2335-2350.
155. Ma, B. and Nussinov, R. (2002) Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Ab16-22, Ab16-35, and Ab10-35): Sequence effects. Proc Natl Acad Sci U S A, 99, 14126-14131.
156. Halperin, I., Ma, B., Wolfson, H. and Nussinov, R. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
157. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S., Wolfson, H. and Nussinov, R. (2001) A hierarchical, building blocks based computational method for protein structure prediction. IBM Journal of Research and Development, Issue on life Science., 45.
158. Tsai, C.J., Ma, B., Sham, Y.Y., Kumar, S. and Nussinov, R. (2001) Structured disorder and conformational selection. Proteins, 44, 418-427.
159. Tsai, C.D., Ma, B., Kumar, S., Wolfson, H. and Nussinov, R. (2001) Protein folding: binding of conformationally fluctuating building blocks via population selection. Crit Rev Biochem Mol Biol, 36, 399-433.
160. Sham, Y.Y., Ma, B., Tsai, C.J. and Nussinov, R. (2001) Molecular dynamics simulation of E-coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations. Protein Sci, 10, 135-148.
161. Ma, B., Wolfson, H.J. and Nussinov, R. (2001) Protein functional epitopes: hot spots, dynamics and combinatorial libraries. Curr Opin Struct Biol, 11, 364-369.
162. Li, W., Ma, B. and Shapiro, B.A. (2001) Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. Journal of Biomolecular Structure & Dynamics, 19, 381-396.
163. Nussinov, R., Ma, B. and Wolfson, H. (2000) Computational methods for docking and drug design:functional epitopes and combinatorial libraries. In Current topics in computational Biology. Ed. T. Jiang, T. Smith, Y. Xu and M.Q. Zhang. MIT Press, Boston, MA.
164. Ma, B., Kumar, S., Tsai, C.J., Wolfson, H., Sinha, N. and Nussinov, R. (2000) Protein-ligand interaction: induced fit? Encyclopedia in life science, London, Macmillan Reference Limited.
165. Ma, B., Lii, J.H. and Allinger, N.L. (2000) Molecular polarizabilities and induced dipole moments in molecular mechanics. Journal of Computational Chemistry, 21, 813-825.
166. Ma, B. and Nussinov, R. (2000) Molecular dynamics simulations of a b-hairpin fragment of protein G: balance between side-chain and backbone forces. J Mol Biol, 296, 1091-1104.
167. Ma, B., Kumar, S., Tsai, C.J., Hu, Z. and Nussinov, R. (2000) Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity? J Theor Biol, 203, 383-397.
168. Ma, B., Tsai, C.J. and Nussinov, R. (2000) A systematic study of the vibrational free energies of polypeptides in folded and random states. Biophys J, 79, 2739-2753.
169. Ma, B., Tsai, C.J. and Nussinov, R. (2000) Binding and folding: in search of intramolecular chaperone-like building block fragments. Protein Eng, 13, 617-627.
170. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Contribution of Salt Bridges Toward Protein Thermostability. J. Biomol. Struc. and Dynamics, conversation 11, 79-85.
171. Kumar, S., Ma, B., Tsai, C.J. and Nussinov, R. (2000) Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins, 38, 368-383.
172. Kumar, S., Ma, B., Tsai, C.J., Sinha, N. and Nussinov, R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci, 9, 10-19.
173. Hu, Z., Ma, B., Wolfson, H. and Nussinov, R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
174. Buyong, Xiong, J., Lubkowski, J. and Nussinov, R. (2000) Homology modeling and molecular dynamics simulations of lymphotactin. Protein Sci, 9, 2192-2199.
175. Tsai, C.J., Kumar, S., Ma, B. and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function. Protein Sci, 8, 1181-1190.
176. Tsai, C.J., Ma, B. and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci U S A, 96, 9970-9972.
177. Ma, B. and Nussinov, R. (1999) Explicit and implicit water simulations of a b-hairpin peptide. Proteins, 37, 73-87.
178. Ma, B., Kumar, S., Tsai, C.J. and Nussinov, R. (1999) Folding funnels and binding mechanisms. Protein Eng, 12, 713-720.
179. Lii, J.H., Ma, B. and Allinger, N.L. (1999) Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Computational Chemistry, 20, 1593-1603.
180. Kumar, S., Ma, B., Tsai, C.J., Wolfson, H. and Nussinov, R. (1999) Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys, 31, 141-164.
181. Ma, B., Schaefer, H.F. and Allinger, N.L. (1998) Theoretical studies of the potential energy surfaces and compositions of the D-aldo- and D-ketohexoses. Journal of the American Chemical Society, 120, 3411-3422.
182. Kirschner, K., Ma, B., Bowen, J. and Duncan, M. (1998) Theoretical investigation of the Ca+N-2 and Ca2+N-2 complexes. CHEMICAL PHYSICS LETTERS, 295, 204-210.
183. King, R.A., Allen, W.D., Ma, B. and Schaefer, H.F. (1998) Fragmentation surface of triplet ketene. Faraday Discussions, 23-50.
184. Ma, B., Schaefer, H.F. and Allinger, N.L. (1997) Computational Studies of Structures and Reactions of Phosphate derivatives. in Recent Research Development in Chemical Science, Transworld Research Network, 1.37.
185. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1997) A molecular mechanics study of the cholesteryl acetate crystal: Evaluation of interconversion among rg, rz, and ra bond lengths. Journal of the American Chemical Society, 119, 2570-2573.
186. Ma, B. and Allinger, N.L. (1997) Calculation of rz structures from rs structures. Journal of Molecular Structure, 413, 395-404.
187. Ma, B., Collins, C.L. and Schaefer, H.F. (1996) Periodic trends for transition metal dihydrides MH2, dihydride dihydrogen complexes MH2* H-2, and tetrahydrides MH4 (M=Ti,V, and Cr). Journal of the American Chemical Society, 118, 870-879.
188. Ma, B., Lii, J.H., Schaefer, H.F. and Allinger, N.L. (1996) Systematic comparison of experimental, quantum mechanical, and molecular mechanical bond lengths for organic molecules. Journal of Physical Chemistry, 100, 8763-8769.
189. Ma, B. and Schaefer, H.F. (1996) Singlet-triplet energy separation and barrier for ring closure for trimethylenemethane and its complexes. Chemical Physics, 207, 31-41.
190. Ma, B., Lii, J.H., Chen, K.S. and Allinger, N.L. (1996) Quantum mechanical and molecular mechanics (MM3) studies of hydrazines. Journal of Physical Chemistry, 100, 11297-11304.
191. Ma, B., Allinger, N.L. and Schaefer, H.F. (1996) Spectroscopic constants and potential energy surfaces for silanone (H2SiO), hydroxysilylene (HSiOH), the hydroxysilylene dimer, and the disilynyl radical (Si2H). Journal of Chemical Physics, 105, 5731-5736.
192. Goldstein, E., Ma, B., Lii, J.H. and Allinger, N.L. (1996) Molecular mechanics calculations (MM3) on nitriles and alkynes. Journal of Physical Organic Chemistry, 9, 191-202.
193. Ma, B., Yamaguchi, Y. and Schaefer, H.F. (1995) Spectroscopic constants and potential energy surfaces for the possible interstellar molecules AlNC and AlCN. Molecular Physics, 86, 1331-1337.
194. Ma, B., Meredith, C. and Schaefer, H.F. (1995) The Quest for a Metaphosphate Intermediate - the Mechanisms for Hydrolysis of Pyrophosphates with and without Catalysis. Journal of Physical Chemistry, 99, 3815-3822.
195. Ma, B., Sulzbach, H.M., Remington, R.B. and Schaefer, H.F. (1995) Structure, Strain-Energy, and Magnetic-Susceptibility of 4-Paracyclophane and the Activation-Energy for Its Interconversion with 1,4-Tetramethylene Dewar Benzene. Journal of the American Chemical Society, 117, 8392-8400.
196. Hu, C.H., Ma, B. and Schaefer, H.F. (1995) The Synchronous Thermal-Decomposition Mechanism of Azoisopropane. Molecular Physics, 85, 769-779.
197. Souter, P.F., Andrews, L., Downs, A.J., Greene, T.M., Ma, B. and Schaefer, H.F. (1994) Observed and Calculated Raman-Spectra of the Ga2H6 and Ga2D6 Molecules. Journal of Physical Chemistry, 98, 12824-12827.
198. Ma, B. and Schaefer, H.F. (1994) Singlet Methylcarbene - Equilibrium Geometry or Transition-State. Journal of the American Chemical Society, 116, 3539-3542.
199. Ma, B., Sulzbach, H.M., Xie, Y.M. and Schaefer, H.F. (1994) p-Electron Delocalization and Compression in Acyclic Acetylenic Precursors to Multidimensional Carbon Networks - Comparison with Experiment for the Recently Synthesized Tris(Trimethylsilyl)-Substituted Tetraethynylmethane - Structures, Thermochemistry, Infrared-Spectra, Polarizabilities, and Hyperpolarizabilities. Journal of the American Chemical Society, 116, 3529-3538.
200. Ma, B. and Schaefer, H.F. (1994) Toward the Observation of Silanone (H2SiO) and Hydroxysilylene (HSiOH) Via Microwave Spectroscopy. Journal of Chemical Physics, 101, 2734-2739.
201. Ma, B., Meredith, C. and Schaefer, H.F. (1994) Pyrophosphate Structures and Reactions - Evaluation of Electrostatic Effects on the Pyrophosphates with and without Alkali Cations. Journal of Physical Chemistry, 98, 8216-8223.
202. Ma, B., Xie, Y.M., Shen, M.Z. and Schaefer, H.F. (1993) PO3-.(H2O)N Clusters - Molecular Anion Structures, Energetics, and Vibrational Frequencies. Journal of the American Chemical Society, 115, 1943-1951.
203. Ma, B., Xie, Y.M., Shen, M.Z., Schleyer, P.V. and Schaefer, H.F. (1993) Isomerization of PO3-*(H2O)N Clusters to H2PO4-*(H2O)N-1 - Transition-States and Barrier Heights. Journal of the American Chemical Society, 115, 11169-11179.
204. Ma, B., Xie, Y.M. and Schaefer, H.F. (1992) Tetraethynylethylene, a Molecule with 4 Very Short C-C Single Bonds - Interpretation of the Infrared-Spectrum. Chemical Physics Letters, 191, 521-526.

1. 提出蛋白质识别的构象选择理论（conformational selection）用以分析蛋白质受体和配体互作，近年来得到广泛接受和应用，成为与经典的“锁与钥匙模型（Lock and key）” 和“诱导契合模型”(Induced Fit)并重 的新药物作用模型。
2. 揭示了蛋白质互作中的热点（hotspot）的结构和序列特征。
3. 利用计算生物学研究蛋白质沉积和聚集物结构,在和阿尔茨海默病密切相关与Aβ和 tau蛋白的淀粉状沉积（amyloid）机理方面做出了大量开创和突出的贡献。率先用分子动力学对抗体识别淀粉状模拟表征。在世界上首次用分子动力学模拟揭示了Aβ淀粉体纤维结构；发现了Aβ42淀粉状纤维新的高清结构，引导了该领域的突破。
4. 提出计算化学作为一种实验手段而不仅仅是模拟工具的哲学思想， http://www.quantum-chemistry-history.com/Hist_Dat/Buyong/The-Philosophy-of-Computational-Quantum-Chemistry.htm

发表论文200多篇，研究结果在蛋白质结构的动态特性与功能表征，酶催化，蛋白质-蛋白质相互作用和药物设计，神经退行性疾病等方面被大量引用，促进了这些领域的发展。 SCI他引共计1万多次。总计第一作者和通讯作者SCI影响因子为500多， H-index 59。