马步勇 长聘教授

邮箱：mabuyong@sjtu.edu.cn



个人简历 研究方向 发表论文 科研成果
1980-1984: 合肥工业大学，化学工程系， 高分子化学工程专业， 学士。
1984-1987: 湖北化学研究所， 高分子化学专业， 硕士。
1987-1991: 湖北化学研究所， 助理研究员。
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。
1995-1998: 美国 佐治亚大学， 化学系 N. L. Allinger 研究组，博士后。
1998-2002：美国国家癌症研究所研究员。
2002-2003： 美国Locus Pharmaceuticals, Inc; Philadelphia, 研究员。
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。
2020： 上海交通大学药学院，教授


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。


https://www.scopus.com/authid/detail.uri?authorId=
2020
1.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, https://doi.org/10.1021/acschemneuro.0c00364 。
2.Derreumaux, P. et al. When Amyloid Proteins Talk to Each Other: a Joint Experimental/Theoretical Perspective on Alzheimer, Parkinson, Type II Diabetes and Amyotrophic Lateral Sclerosis Diseases, Chem. Rev. in revision.
3.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. in revision.
2019
4.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 Mar; 33(3): 4225–4235.
5.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 Feb 15; 79(4): 807–818.
6.Guven-Maiorov, E., Tsai, C.J., Ma, B. and Nussinov, R. Interface-Based Structural Prediction of Novel Host-Pathogen Interactions. Methods Mol Biol, 1851, 317-335.
7.H Luo, L Hu, B Ma, M Zhao, M Luo, Q Deng, S Deng, H Ye, T Lin, J Chen, 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
8.E Guven-Maiorov, CJ Tsai, B Ma, R Nussinov Interface-based structural prediction of novel host-pathogen interactions. Computational Methods in Protein Evolution, 2019, 317-335
9.Zhao, J., Nussinov, R. and Ma, B. Antigen binding allosterically promotes Fc receptor recognition. MAbs, 11 (1), 58-74
2018
10.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
11.M Zhang, J Zheng, R Nussinov, B Ma Molecular recognition between Aβ-specific single-domain antibody and Aβ Misfolded aggregates. Antibodies 7 (3), 25
12.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.
13.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.
14.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
15.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.
16.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.
17. 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.
18.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.
19.J Zhao, R Nussinov, WJ Wu, B Ma In silico methods in antibody design Antibodies 7 (3), 22
2017
20.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.
21.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.
22.Dong, X., Sun, Y., Wei, G., Nussinov, R. and Ma, B.* (2017) Binding of protofibrillar A? trimers to lipid bilayer surface enhances A? structural stability and causes membrane thinning Phys Chem Chem Phys. 19, 27556-27569.
23.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.
24.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
25.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.
26.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.
27.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.
28.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.
29.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
30.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.
31.166.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.
32.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.
33.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, e**.
34.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.
35.Ma, B. and Nussinov, R. (2016) Protein dynamics: Conformational footprints. Nat Chem Biol, 12, 890-891.
36.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.
37.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.
38.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.
39.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.
40.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.
41.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
42.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.
43.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.
44.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.
45.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.
46.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, e**.
47.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.
48.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.
49.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.
50.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.
51.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.
52.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
53.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.
54.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.
55.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.
56.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.
57.Ma, B. and Nussinov, R. (2014) Druggable orthosteric and allosteric hot spots to target protein-protein interactions. Curr Pharm Des, 20, 1293-1301.
58.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.
59.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.
60.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.
61.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.
62.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.
63.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.
64.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
65.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.
66.Nussinov, R., Tsai, C.J. and Ma, B. (2013) The underappreciated role of allostery in the cellular network. Annu Rev Biophys, 42, 169-189.
67.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.
68.Ma, B. and Nussinov, R. (2013) Structured crowding and its effects on enzyme catalysis. Top Curr Chem, 337, 123-137.
69.Nussinov, R., Ma, B., Tsai, C.J. and Csermely, P. (2013) Allosteric conformational barcodes direct signaling in the cell. Structure, 21, 1509-1521.
70.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.
71.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
72.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.
73.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.
74.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.
75.Nussinov, R. and Ma, B. (2012) Protein dynamics and conformational selection in bidirectional signal transduction. BMC Biol, 10, 2.
76.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.
77.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
78.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.
79.Ma, B., Tsai, C.J., Haliloglu, T. and Nussinov, R. (2011) Dynamic allostery: linkers are not merely flexible. Structure, 19, 907-917.
80.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.
81.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.
82.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.
83.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
84.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.
85.Ma, B. and Nussinov, R. (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol, 14, 652-659.
86.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.
87.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.
88.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.
89.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.
90.Pan, Y., Tsai, C.J., Ma, B. and Nussinov, R. (2010) Mechanisms of transcription factor selectivity. Trends Genet, 26, 75-83.
Selected papers before 2009
91.Ma, B. and Nussinov, R. (2009) Regulating highly dynamic unstructured proteins and their coding mRNAs. Genome Biol, 10, 204.
92.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.
93.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.
94.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.
95.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.
96.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.
97.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.
98.Ma, B. and Nussinov, R. (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol.
99.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.
100.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.
101.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.
102.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.
103.Gunasekaran, K., Ma, B. and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins, 57, 433-443.
104.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.
105.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.
106.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.
107.Ma, B. and Nussinov, R. (2002) Molecular dynamics simulations of alanine rich b-sheet oligomers: Insight into amyloid formation. Protein Sci, 11, 2335-2350.
108.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.
109.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.
110.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.
111.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.
112.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.
113.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.
114.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.
115.Hu, Z., Ma, B., Wolfson, H. and Nussinov, R. (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins, 39, 331-342.
116.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.
117.Ma, B., Kumar, S., Tsai, C.J. and Nussinov, R. (1999) Folding funnels and binding mechanisms. Protein Eng, 12, 713-720.
118.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.
119.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.
120.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.
121.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.
122.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.
123.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.
124.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.
125.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.
126.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SCI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。