Ma, Buyong

Principles of docking: An overview of search algorithms and a guide to scoring functions

Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 1,294

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

Keskin, O., Gursoy, A., Ma, B., & Nussinov, R. (2008) · Chemical Reviews

Protein Structure and DynamicsBioinformatics and Genomic Networks

Cited by 697

Folding funnels, binding funnels, and protein function

Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 648

Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces

Ma, B., Elkayam, T., Wolfson, H., & Nussinov, R. (2003) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 595

Folding and binding cascades: Dynamic landscapes and population shifts

Kumar, S., Ma, B., Tsai, C., Sinha, N., & Nussinov, R. (2000) · Protein Science

Protein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

Cited by 595

Folding funnels and binding mechanisms

Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection

Protein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

Cited by 594

Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

Keskin, O., Ma, B., & Nussinov, R. (2005) · Journal of Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 519

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 436

Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations

Ma, B., Shatsky, M., Wolfson, H. J., & Nussinov, R. (2002) · Protein Science

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 420

Folding and binding cascades: Shifts in energy landscapes

Tsai, C.-J., Ma, B., & Nussinov, R. (1999) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 365

Dynamic Allostery: Linkers Are Not Merely Flexible

Ma, B., Tsai, C.-J., Haliloğlu, T., & Nussinov, R. (2011) · Structure

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 222

Structured disorder and conformational selection

Tsai, C., Ma, B., Sham, Y. Y., Kumar, S., & Nussinov, R. (2001) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 202

Protein–protein interaction networks: how can a hub protein bind so many different partners?

Tsai, C.-J., Ma, B., & Nussinov, R. (2009) · Trends in Biochemical Sciences

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 138

Folding funnels and conformational transitions via hinge-bending motions

Kumar, S., Ma, B., Tsai, C.-J., Wolfson, H., & Nussinov, R. (1999) · Cell Biochemistry and Biophysics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 94

Transition-state Ensemble in Enzyme Catalysis: Possibility, Reality, or Necessity?

MA, B., KUMAR, S., TSAI, C.-J., HU, Z., & NUSSINOV, R. (2000) · Journal of Theoretical Biology

Protein Structure and DynamicsPhysical Organic Chemistry and Reaction Kinetics

Cited by 86

Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau

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) · Journal of the American Chemical Society

Alzheimer's disease research and treatmentsElectron Spin Resonance Studies

Cited by 75

Visualizing RNA conformational and architectural heterogeneity in solution

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) · Nature Communications

RNA and protein synthesis mechanismsProtein Structure and Dynamics

Cited by 66

Protein dynamics and conformational selection in bidirectional signal transduction

Nussinov, R., & Ma, B. (2012) · BMC Biology

Axon Guidance and Neuronal SignalingProtein Structure and Dynamics

Cited by 65

Allosteric Conformational Barcodes Direct Signaling in the Cell

Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 55

Promiscuous and specific recognition among ephrins and Eph receptors

Dai, D., Huang, Q., Nussinov, R., & Ma, B. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Axon Guidance and Neuronal SignalingProtein Structure and Dynamics

Cited by 51

Druggable Orthosteric and Allosteric Hot Spots to Target Protein-protein Interactions

Ma, B., & Nussinov, R. (2014) · Current Pharmaceutical Design

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 45

Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms

Weismiller, H. A., Murphy, R., Wei, G., Ma, B., Nussinov, R., & Margittai, M. (2018) · Journal of Biological Chemistry

Alzheimer's disease research and treatmentsPrion Diseases and Protein Misfolding

Cited by 44

Single Mutations in Tau Modulate the Populations of Fibril Conformers through Seed Selection

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) · Angewandte Chemie International Edition

Alzheimer's disease research and treatmentsPrion Diseases and Protein Misfolding

Cited by 42

Amplification of signaling via cellular allosteric relay and protein disorder

Ma, B., & Nussinov, R. (2009) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 36