Nussinov, Ruth

PatchDock and SymmDock: servers for rigid and symmetric docking

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 3,018

The role of dynamic conformational ensembles in biomolecular recognition

Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 2,008

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

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences

Protein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

Cited by 821

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

Artificial intelligence in COVID-19 drug repurposing

Zhou, Y., Wang, F., Tang, J., Nussinov, R., & Cheng, F. (2020) · The Lancet Digital Health

Computational Drug Discovery MethodsArtificial Intelligence in Healthcare and Education

Cited by 636

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

Allostery: Absence of a change in shape does not imply that allostery is not at play

Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 453

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

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 404

A Unified View of “How Allostery Works”

Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology

Receptor Mechanisms and SignalingProtein Structure and Dynamics

Cited by 401

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

Target identification among known drugs by deep learning from heterogeneous networks

Zeng, X., Zhu, S., Lu, W., Liu, Z., Huang, J., Zhou, Y., Fang, J., Huang, Y., Guo, H., Li, L., et al. (2020) · Chemical Science

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 357

Ras Conformational Ensembles, Allostery, and Signaling

Lu, S., Jang, H., Muratcioglu, S., Gursoy, A., Keskin, O., Nussinov, R., & Zhang, J. (2016) · Chemical Reviews

Protein Kinase Regulation and GTPase SignalingReceptor Mechanisms and Signaling

Cited by 355

Deep generative molecular design reshapes drug discovery

Zeng, X., Wang, F., Luo, Y., Kang, S.-G., Tang, J., Lightstone, F. C., Fang, E. F., Cornell, W., Nussinov, R., & Cheng, F. (2022) · Cell Reports Medicine

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 295

Allostery: An Overview of Its History, Concepts, Methods, and Applications

Liu, J., & Nussinov, R. (2016) · PLOS Computational Biology

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 281

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

The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B

Lu, S., Jang, H., Nussinov, R., & Zhang, J. (2016) · Scientific Reports

Protein Kinase Regulation and GTPase SignalingProtein Structure and Dynamics

Cited by 219

Allosteric post-translational modification codes

Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012) · Trends in Biochemical Sciences

Protein Structure and DynamicsAdvanced Proteomics Techniques and Applications

Cited by 211