Protein interface conservation across structure space

Comparative Protein Modelling by Satisfaction of Spatial Restraints

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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BioGRID: a general repository for interaction datasets

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Data growth and its impact on the SCOP database: new developments

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IntAct--open source resource for molecular interaction data

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PQS: a protein quaternary structure file server

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ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

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Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases

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Structure-Based Assembly of Protein Complexes in Yeast

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A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

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Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

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The Relationship Between Sequence and Interaction Divergence in Proteins

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Prediction of interface residues in protein–protein complexes by a consensus neural network method: Test against NMR data

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Protein–protein docking benchmark version 3.0

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Computational Prediction of Protein–Protein Interactions

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MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading

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Protein binding site prediction using an empirical scoring function

Liang, S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl454 · Cited by 237 · see citing works

GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences

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Supersites within superfolds. Binding site similarity in the absence of homology 1 1Edited by J. Thornton

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An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance

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High‐throughput two‐hybrid analysis

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Interaction-site prediction for protein complexes: a critical assessment

Zhou, H., & Qin, S. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm323 · Cited by 170 · see citing works

The geometry of domain combination in proteins 1 1Edited by J. Thornton

Bashton, M., & Chothia, C. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5288 · Cited by 140 · see citing works

Computational methods of analysis of protein–protein interactions

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Protein-Protein Interfaces: Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Their Similarities and Differences

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The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry

Kim, W., Henschel, A., Winter, C., & Schroeder, M. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020124 · Cited by 112 · see citing works

Structural relationships among proteins with different global topologies and their implications for function annotation strategies

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Finding biologically relevant protein domain interactions: Conserved binding mode analysis

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Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways

Keskin, Ö., & Nussinov, R. (2005) · Protein Engineering Design and Selection · doi:10.1093/protein/gzh095 · Cited by 75 · see citing works

Connecting the Protein Structure Universe by Using Sparse Recurring Fragments

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Divergence of Interdomain Geometry in Two-Domain Proteins

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Protein complex compositions predicted by structural similarity

Davis, F. P. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl353 · Cited by 57 · see citing works

The Third CAPRI Assessment Meeting Toronto, Canada, April 20–21, 2007

Janin, J., & Wodak, S. J. (2007) · Structure · doi:10.1016/j.str.2007.06.007 · Cited by 49 · see citing works

Localization of protein‐binding sites within families of proteins

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Conservation of Orientation and Sequence in Protein Domain–Domain Interactions

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Survey of the geometric association of domain–domain interfaces

Kim, W., & Ison, J. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20693 · Cited by 28 · see citing works

Biological Units and their Effect upon the Properties and Prediction of Protein–Protein Interactions

Jefferson, E., Walsh, T. P., & Barton, G. J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.09.042 · Cited by 21 · see citing works

Fragnostic: walking through protein structure space

Friedberg, I., & Godzik, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki363 · Cited by 21 · see citing works

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · see citing works

Structure-based prediction of protein–protein interactions on a genome-wide scale

Zhang, Q. C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C. A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., et al. (2012) · Nature · doi:10.1038/nature11503 · Cited by 723 · see citing works

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

Tubiana, J., Schneidman-Duhovny, D., & Wolfson, H. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01490-7 · Cited by 274 · see citing works

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Gao, M., Nakajima An, D., Parks, J. M., & Skolnick, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29394-2 · Cited by 252 · see citing works

Templates are available to model nearly all complexes of structurally characterized proteins

Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200678109 · Cited by 179 · see citing works

Structural space of protein–protein interfaces is degenerate, close to complete, and highly connected

Gao, M., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012820107 · Cited by 139 · see citing works

RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

Walia, R. R., Xue, L. C., Wilkins, K., El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097725 · Cited by 132 · see citing works

Low-resolution structural modeling of protein interactome

Vakser, I. A. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.12.003 · Cited by 62 · see citing works

Are protein-protein interfaces special regions on a protein’s surface?

Tonddast-Navaei, S., & Skolnick, J. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4937428 · Cited by 31 · see citing works

How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking

Chakravarty, D., McElfresh, G., Kundrotas, P. J., & Vakser, I. A. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25875 · Cited by 13 · see citing works

Structural bioinformatics: Deriving biological insights from protein structures

Chandra, N. R., Anand, P., & Yeturu, K. (2010) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-010-0045-6 · Cited by 14 · see citing works

Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily

Guardino, K. M., Sheftic, S. R., Slattery, R. E., & Alexandrescu, A. T. (2009) · International Journal of Molecular Sciences · doi:10.3390/ijms10052412 · Cited by 12 · see citing works

Protein structural motifs in prediction and design

Mackenzie, C. O., & Grigoryan, G. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.03.012 · Cited by 42 · see citing works

New era in structural biology with the AlphaFold program

Miyazono, K., & Tanokura, M. (2022) · Translational and Regulatory Sciences · doi:10.33611/trs.2022-005 · Cited by 2 · see citing works

Protein Structural Changes Based on Structural Comparison

Koike, R., & Ota, M. (2021) · Springer eBooks · doi:10.1007/978-981-16-5812-9_8