Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

Book Review: Pattern Recognition and Machine Learning

Nasrabadi, N. M. (2007) · Journal of Electronic Imaging · doi:10.1117/1.2819119 · Cited by 22,066

STRING v10: protein–protein interaction networks, integrated over the tree of life

Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K. P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1003 · Cited by 10,436

Inference of Macromolecular Assemblies from Crystalline State

Krissinel, E., & Henrick, K. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.022 · Cited by 10,007

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706

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

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566

Human Protein Reference Database--2009 update

Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, R. B., Venugopal, A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn892 · Cited by 3,252

PatchDock and SymmDock: servers for rigid and symmetric docking

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018

The FoldX web server: an online force field

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759

Principles of protein-protein interactions

Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684

Intrinsically disordered protein

Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., Oldfield, C. J., Campen, A. M., Ratliff, C. M., Hipps, K. W., et al. (2001) · Journal of Molecular Graphics and Modelling · doi:10.1016/s1093-3263(00)00138-8 · Cited by 2,272

The Database of Interacting Proteins: 2004 update

Salwinski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh086 · Cited by 2,271

Classification of Intrinsically Disordered Regions and Proteins

van der Lee, R., Buljan, M., Lang, B., Weatheritt, R. J., Daughdrill, G. W., Dunker, A. K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D. T., et al. (2014) · Chemical Reviews · doi:10.1021/cr400525m · Cited by 2,249

A draft map of the human proteome

Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198

Protein structure prediction and analysis using the Robetta server

Kim, D. E., Chivian, D. C., & Baker, D. A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh468 · Cited by 2,099

Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

Wells, J. A., & McClendon, C. L. (2007) · Nature · doi:10.1038/nature06526 · Cited by 2,002

Anatomy of hot spots in protein interfaces

Bogan, A. A., & Thorn, K. S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1843 · Cited by 1,988

A Hot Spot of Binding Energy in a Hormone-Receptor Interface

Clackson, T., & Wells, J. A. (1995) · Science · doi:10.1126/science.7529940 · Cited by 1,987

Crystal structure of the ribosome at 5.5 Å resolution

Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

Orchard, S. E., Ammari, M. G., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F. C., Campbell, N. H., Chavali, G. B., Chen, C. C. L., del‐Toro, N., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1115 · Cited by 1,845

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben‐Tal, N. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq399 · Cited by 1,822

Mass-spectrometry-based draft of the human proteome

Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820

ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

Pierce, B. G., Wiehe, K. J., Hwang, H., Kim, B., Vreven, T., & Weng, Z. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu097 · Cited by 1,767

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

Pellegrini, M. A., Marcotte, E. M., Thompson, M. J., Eisenberg, D. S., & Yeates, T. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4285 · Cited by 1,568

Uncovering disease-disease relationships through the incomplete interactome

Menche, J., Sharma, A., Kitsak, M., Ghiassian, S. D., Vidal, M., Loscalzo, J., & Barabási, A.-L. (2015) · Science · doi:10.1126/science.1257601 · Cited by 1,546

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392

The HADDOCK web server for data-driven biomolecular docking

de Vries, S. J., van Dijk, M., & Bonvin, A. M. J. J. (2010) · Nature Protocols · doi:10.1038/nprot.2010.32 · Cited by 1,387

A Proteome-Scale Map of the Human Interactome Network

Rolland, T., Taşan, M., Charloteaux, B., Pevzner, S. J., Zhong, Q., Sahni, N., Yi, S. S., Lemmens, I. H., Fontanillo, C., Mosca, R., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.050 · Cited by 1,381

CORUM: the comprehensive resource of mammalian protein complexes—2009

Ruepp, A., Wägele, B., Lechner, M., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., & Mewes, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp914 · Cited by 1,299

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

Xu, Z. S., Horwich, A. L., & Sigler, P. B. (1997) · Nature · doi:10.1038/41944 · Cited by 1,244

Ensembl 2014

Flicek, P., Amode, M. R., Barrell, D. G., Beal, K. M., Billis, K., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G. M. P., Fitzgerald, S. F., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1196 · Cited by 1,242

Protein interaction maps for complete genomes based on gene fusion events

Enright, A. J., Iliopoulos, I., Kyrpides, N. C., & Ouzounis, C. A. (1999) · Nature · doi:10.1038/47056 · Cited by 1,072

MINT, the molecular interaction database: 2012 update

Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A. P., Santonico, E., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr930 · Cited by 1,062

Conservation of gene order: a fingerprint of proteins that physically interact

Dandekar, T. (1998) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01274-2 · Cited by 1,047

Identification of direct residue contacts in protein–protein interaction by message passing

Weigt, M., White, R. A., Szurmant, H., Hoch, J. A., & Hwa, T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805923106 · Cited by 1,025

Predicting protein–protein interactions based only on sequences information

Shen, J., Zhang, J., Luo, X., Zhu, W., Yu, K., Chen, K., Li, Y., & Jiang, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607879104 · Cited by 996

A human phenome-interactome network of protein complexes implicated in genetic disorders

Lage, K., Karlberg, E., Størling, Z. M., Olason, P., Pedersen, A., Rigina, O., Hinsby, A., Tümer, Z., Pociot, F., Tommerup, N., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1295 · Cited by 973

Diversity of protein–protein interactions

Nooren, I. M. A., & Thornton, J. (2003) · EMBO Journal · doi:10.1093/emboj/cdg359 · Cited by 942

An empirical framework for binary interactome mapping

Venkatesan, K., Rual, J.-F. M., Vázquez, A., Stelzl, U., Lemmens, I. H., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1280 · Cited by 925

The BioGRID interaction database: 2015 update

Chatr‐aryamontri, A., Breitkreutz, B., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., Stark, C., Breitkreutz, A., Kolas, N. K., O’Donnell, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1204 · Cited by 911

Estimating the size of the human interactome

Stumpf, M. P. H., Thorne, T., de Silva, E., Stewart, R., An, H. J., Lappé, M., & Wiuf, C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708078105 · Cited by 858

ClusPro: an automated docking and discrimination method for the prediction of protein complexes

Comeau, S. R., GATCHELL, D. W., Vajda, S., & Camacho, C. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg371 · Cited by 857

A simple physical model for binding energy hot spots in protein–protein complexes

Kortemme, T., & Baker, D. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202485799 · Cited by 818

Native mass spectrometry: a bridge between interactomics and structural biology

Heck, A. J. R. (2008) · Nature Methods · doi:10.1038/nmeth.1265 · Cited by 766

Global landscape of HIV–human protein complexes

Jäger, S., Cimermancic, P., Gulbahce, N., Johnson, J. R., McGovern, K. E., Clarke, S. C., Shales, M., Mercenne, G., Pache, L., Li, K., et al. (2012) · Nature · doi:10.1038/nature10719 · Cited by 731

Methods for the detection and analysis of protein–protein interactions

Berggård, T., Linse, S. S., & James, P. (2007) · PROTEOMICS · doi:10.1002/pmic.200700131 · Cited by 714

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 · doi:10.1021/cr040409x · Cited by 697

FireDock: Fast interaction refinement in molecular docking

Andrusier, N., Nussinov, R., & Wolfson, H. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21495 · Cited by 679

ConsensusPathDB: toward a more complete picture of cell biology

Kamburov, A., Pentchev, K., Galicka, H., Wierling, C., Lehrach, H., & Herwig, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1156 · Cited by 671

Reactome: a knowledge base of biologic pathways and processes

Västrik, I., D’Eustachio, P., Schmidt, E., Geeta, J.-T., Gopinath, G., Croft, D. W., de Bono, B., Gillespie, M. E., Jassal, B., Lewis, S., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r39 · Cited by 662

Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint

Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

Kozakov, D., Grove, L. E., Hall, D. R., Bohnuud, T., Mottarella, S. E., Luo, L., Xia, B., Beglov, D., & Vajda, S. (2015) · Nature Protocols · doi:10.1038/nprot.2015.043 · Cited by 654

PDBsum: a web-based database of summaries and analyses of all PDB structures

Laskowski, R. A., Hutchinson, E. G., Michie, A. D., Wallace, A. C., Jones, M. L., & Thornton, J. M. (1997) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(97)01140-7 · Cited by 648

Scoring residue conservation

Valdar, W. S. J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10146 · Cited by 633

Visualization of omics data for systems biology

Gehlenborg, N., O’Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1436 · Cited by 629

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 · doi:10.1073/pnas.1030237100 · Cited by 595

The RosettaDock server for local protein-protein docking

Lyskov, S., & Gray, J. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn216 · Cited by 593

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

Ge, H., Liu, Z., Church, G. M., & Vidal, M. (2001) · Nature Genetics · doi:10.1038/ng776 · Cited by 575

Exploiting indirect neighbours and topological weight to predict protein function from protein–protein interactions

Chua, H. N., Sung, W.-K. K., & Wong, L. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl145 · Cited by 571

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

Kastritis, P. L., & Bonvin, A. M. J. J. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2012.0835 · Cited by 547

The MIPS mammalian protein–protein interaction database

Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stümpflen, V., Mewes, H., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti115 · Cited by 541

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Orchard, S. E., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S. L., Bridge, A. J., Briganti, L., Brinkman, F. S. L., Cesareni, G., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1931 · Cited by 538

Similarity of phylogenetic trees as indicator of protein–protein interaction

Pazos, F., & Valencia, A. (2001) · Protein Engineering Design and Selection · doi:10.1093/protein/14.9.609 · Cited by 521

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 · doi:10.1016/j.jmb.2004.10.077 · Cited by 519

Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife · doi:10.7554/elife.03430 · Cited by 515

Interactome3D: adding structural details to protein networks

Mosca, R., Céol, A., & Aloy, P. (2013) · Nature Methods · doi:10.1038/nmeth.2289 · Cited by 479

Protein–protein docking benchmark version 4.0

Hwang, H., Vreven, T., Janin, J., & Weng, Z. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22830 · Cited by 474

Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights

Kim, P. M., Lu, L. J., Xia, Y., & Gerstein, M. (2006) · Science · doi:10.1126/science.1136174 · Cited by 471

Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., & Aebersold, R. H. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r000001-mcp201 · Cited by 468

ZRANK: Reranking protein docking predictions with an optimized energy function

Pierce, B., & Weng, Z. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21373 · Cited by 468

A dissection of specific and non-specific protein-protein interfaces.

Bahadur, R., Chakrabarti, P., Rodier, F., & Janin, J. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.073 · Cited by 464

An experimentally derived confidence score for binary protein-protein interactions

Falter‐Braun, P., Tasan, M., Dreze, M., Barrios‐Rodiles, M., Lemmens, I. H., Yu, H., Sahalie, J. M., Murray, R. R., Roncari, L., de Smet, A.-S., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1281 · Cited by 444

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

Neuvirth, H., Raz, R., & Schreiber, G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.040 · Cited by 436

Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., et al. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.07.016 · Cited by 424

Mass Spectrometry–Based Proteomics and Network Biology

Bensimon, A., Heck, A. J. R., & Aebersold, R. H. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072909-100424 · Cited by 421

Functional topology in a network of protein interactions

Pržulj, N., Wigle, D. A., & Jurišica, I. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg415 · Cited by 415

How complete are current yeast and human protein-interaction networks?

Hart, T., Ramani, A. K., & Marcotte, E. M. (2006) · Genome biology · doi:10.1186/gb-2006-7-11-120 · Cited by 407

ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions

Thorn, K. S., & Bogan, A. A. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.3.284 · Cited by 403

Assessing experimentally derived interactions in a small world

Goldberg, D. S., & Roth, F. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0735871100 · Cited by 399

Structure, function, and evolution of transient and obligate protein–protein interactions

Mintseris, J., & Weng, Z. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502667102 · Cited by 373

pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking

Cheng, T. M. K., Blundell, T. L., & Fernández‐Recio, J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21419 · Cited by 341

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

Schaefer, M. H., Fontaine, J., Vinayagam, A., Porras, P., Wanker, E. E., & Andrade-Navarro, M. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031826 · Cited by 340

Phosphorylation in protein-protein binding: effect on stability and function

Nishi, H., Hashimoto, K., & Panchenko, A. R. (2011) · Structure · doi:10.1016/j.str.2011.09.021 · Cited by 322

Protein-Protein Docking: From Interaction to Interactome

Vakser, I. A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.08.033 · Cited by 318

A structure‐based benchmark for protein–protein binding affinity

Kastritis, P., Moal, I., Hwang, H., Weng, Z., Bates, P. A., Bonvin, A., & Janin, J. (2011) · Protein Science · doi:10.1002/pro.580 · Cited by 318

3did: a catalog of domain-based interactions of known three-dimensional structure

Mosca, R., Ceol, A. G. M., Stein, A., Olivella, R., & Aloy, P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt887 · Cited by 307

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., & Gray, J. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022477 · Cited by 306

Computational alanine scanning of the 1:1 human growth hormone–receptor complex

Huo, S., Massova, I., & Kollman, P. A. (2001) · Journal of Computational Chemistry · doi:10.1002/jcc.1153 · Cited by 305

PDBsum additions

de Beer, T., Berka, K., Thornton, J. M., & Laskowski, R. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt940 · Cited by 300

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

Yeger‐Lotem, E., Riva, L., Su, L. J., Gitler, A. D., Cashikar, A. G., King, O. D., Auluck, P. K., Geddie, M. L., Valastyan, J. S., Karger, D. R., et al. (2009) · Nature Genetics · doi:10.1038/ng.337 · Cited by 287

SwarmDock: a server for flexible protein–protein docking

Torchala, M., Moal, I. H., Chaleil, R. A. G., Fernández‐Recio, J., & Bates, P. A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt038 · Cited by 285

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Moal, I. H., & Fernández-Recio, J. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts489 · Cited by 281

Dissecting subunit interfaces in homodimeric proteins

Bahadur, R. P., Chakrabarti, P., Rodier, F., & Janin, J. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10461 · Cited by 280

Transient protein-protein interactions

Acuner, S. E., Engin, H. B., Gürsoy, A., & Keskin, Ö. (2011) · Protein Engineering Design and Selection · doi:10.1093/protein/gzr025 · Cited by 275

Protein binding specificity versus promiscuity

Schreiber, G., & Keating, A. E. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.10.002 · Cited by 268

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

Tunçbağ, N., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2011) · Nature Protocols · doi:10.1038/nprot.2011.367 · Cited by 264

Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy

Tunçbağ, N., Gürsoy, A., & Keskin, Ö. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp240 · Cited by 259

Protein–Protein Interaction Hotspots Carved into Sequences

Ofran, Y., & Rost, B. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030119 · Cited by 258

ISIS: interaction sites identified from sequence

Ofran, Y., & Rost, B. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl303 · Cited by 257

Docking, scoring, and affinity prediction in CAPRI

Lensink, M. F., & Wodak, S. J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24428 · Cited by 249

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

Marsh, J. A., Hernández, H., Hall, Z., Ahnert, S. E., Perica, T., Robinson, C. V., & Teichmann, S. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.044 · Cited by 248

In silico two‐hybrid system for the selection of physically interacting protein pairs

Pazos, F., & Valencia, A. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10074 · Cited by 243

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

Lu, L. J., Lu, H. J., & Skolnick, J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10222 · Cited by 242

PrePPI: a structure-informed database of protein–protein interactions

Zhang, Q. C., Petrey, D. S., Garzón, J. I., Deng, L., & Honig, B. H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1231 · Cited by 240

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Kar, G., Gursoy, A., & Keskin, O. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000601 · Cited by 235

Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)

Morelli, X., Bourgeas, R., & Roche, P. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.05.024 · Cited by 223

KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features

Zhu, X., & Mitchell, J. C. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23094 · Cited by 221

Diversity in GeneticIn VivoMethods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System

Stynen, B., Tournu, H., Tavernier, J. H., & Dijck, P. V. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05021-11 · Cited by 218

Protein–Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking

Li, X., Keskin, Ö., Ma, B., Nussinov, R., & Liang, J. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.09.051 · Cited by 217

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

Turner, B., Razick, S., Turinsky, A. L., Vlasblom, J., Crowdy, E., Cho, E., Morrison, K., Donaldson, I. M., & Wodak, S. J. (2010) · Database · doi:10.1093/database/baq023 · Cited by 211

NOXclass: prediction of protein-protein interaction types

Zhu, H., Domingues, F. S., Sommer, I., & Lengauer, T. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-27 · Cited by 210

Specific versus non-specific contacts in protein crystals

Janin, J. (1997) · Nature Structural Biology · doi:10.1038/nsb1297-973 · Cited by 206

HotPoint: hot spot prediction server for protein interfaces

Tunçbağ, N., Keskin, Ö., & Gürsoy, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq323 · Cited by 206

Protein-protein interaction networks and biology—what's the connection?

Hakes, L., Pinney, J. W., Robertson, D. L., & Lovell, S. C. (2008) · Nature Biotechnology · doi:10.1038/nbt0108-69 · Cited by 200

A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications

Keskin, Ö., Tsai, C., Wolfson, H. J., & Nussinov, R. (2004) · Protein Science · doi:10.1110/ps.03484604 · Cited by 197

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

Blohm, P., Frishman, G., Smialowski, P., Goebels, F., Wachinger, B., Ruepp, A., & Frishman, D. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1079 · Cited by 192

Targeting Protein-Protein Interactions with Small Molecules: Challenges and Perspectives for omputational Binding Epitope Detection and Ligand Finding

González-Ruiz, D., & Gohlke, H. (2006) · Current Medicinal Chemistry · doi:10.2174/092986706778201530 · Cited by 190

FiberDock: Flexible induced‐fit backbone refinement in molecular docking

Mashiach, E., Nussinov, R., & Wolfson, H. J. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22668 · Cited by 187

InterProSurf: a web server for predicting interacting sites on protein surfaces

Negi, S. S., Schein, C. H., Oezguen, N., Power, T. D., & Braun, W. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm474 · Cited by 187

Functional advantages of dynamic protein disorder

Berlow, R. B., Dyson, H. J., & Wright, P. E. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.06.003 · Cited by 184

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps

Huang, H., Jedynak, B. M., & Bader, J. S. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030214 · Cited by 182

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

Huang, S. C., & Fraenkel, E. (2009) · Science Signaling · doi:10.1126/scisignal.2000350 · Cited by 181

meta-PPISP: a meta web server for protein-protein interaction site prediction

Qin, S., & Zhou, H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm434 · Cited by 181

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

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

Mukherjee, S., & Zhang, Y. (2011) · Structure · doi:10.1016/j.str.2011.04.006 · Cited by 174

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

Finn, R. D., Miller, B. L., Clements, J., & Bateman, A. G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1210 · Cited by 169

DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions

ger, D. M. K. ⁄., & Gohlke, H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq471 · Cited by 169

Template-based structure modeling of protein–protein interactions

Szilágyi, A., & Zhang, Y. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.11.005 · Cited by 168

SCOPPI: a structural classification of protein–protein interfaces

Winter, C., Henschel, A., Kim, W., & Schroeder, M. (2005) · Nucleic Acids Res. · doi:10.1093/nar/gkj099 · Cited by 167

Protein–protein docking tested in blind predictions: the CAPRI experiment

Janin, J. (2010) · Molecular BioSystems · doi:10.1039/c005060c · Cited by 166

The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces

Fischer, T. B., Arunachalam, K. V., Bailey, D., Mangual, V., Bakhru, S., Russo, R., Huang, D. S., Paczkowski, M., Lalchandani, V., Ramachandra, C., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg163 · Cited by 164

Conservation helps to identify biologically relevant crystal contacts

Valdar, W. S. J., & Thornton, J. M. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5034 · Cited by 162

KFC Server: interactive forecasting of protein interaction hot spots

Darnell, S. J., LeGault, L., & Mitchell, J. C. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn346 · Cited by 149

2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions

Basse, M. J., Betzi, S., Bourgeas, R., Bouzidi, S., Chetrit, B., Hamon, V., Morelli, X., & Roche, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1002 · Cited by 148

Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases

Pogoryelov, D., Krah, A., Langer, J. D., Yıldız, Ö., Faraldo‐Gómez, J. D., & Meier, T. W. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.457 · Cited by 145

HitPredict: a database of quality assessed protein–protein interactions in nine species

Patil, A., Nakai, K., & Nakamura, H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq897 · Cited by 145

Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways

Keskin, O., & Nussinov, R. (2007) · Structure · doi:10.1016/j.str.2007.01.007 · Cited by 144

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

Meyer, M. J., Das, J., Wang, X., & Yu, H. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt181 · Cited by 144

Structural, Evolutionary, and Assembly Principles of Protein Oligomerization

Levy, E. D., & Teichmann, S. A. (2013) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-386931-9.00002-7 · Cited by 143

Protein interface classification by evolutionary analysis

Duarte, J. M., Srebniak, A., Schärer, M. A., & Capitani, G. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-334 · Cited by 141

WHISCY: What information does surface conservation yield? Application to data‐driven docking

de Vries, S. J., van Dijk, A. D. J., & Bonvin, A. M. J. J. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20842 · Cited by 140

Two-hybrid technologies in proteomics research

Suter, B., Kittanakom, S., & Štagljar, I. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.06.005 · Cited by 140

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

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach

Singh, R., Park, D., Xu, J., Hosur, R., & Berger, B. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq481 · Cited by 136

PAIRpred: Partner‐specific prediction of interacting residues from sequence and structure

Minhas, F., Geiss, B. J., & Ben‐Hur, A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24479 · Cited by 127

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together

Jayapandian, M., Chapman, A. P., Tarcea, V. G., Yu, C., Elkiss, A., Ianni, A. M., Liu, B., Nandi, A., Santos, C., Andrews, P., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl859 · Cited by 125

Ras signaling from plasma membrane and endomembrane microdomains

Plowman, S. J., & Hancock, J. F. (2005) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2005.06.004 · Cited by 124

Recent advances in charting protein–protein interaction: mass spectrometry-based approaches

Gavin, A., Maeda, K., & Kühner, S. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.09.007 · Cited by 124

HotSprint: database of computational hot spots in protein interfaces

Güney, E., Tunçbağ, N., Keskin, Ö., & Gürsoy, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm813 · Cited by 115

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

Tunçbağ, N., Braunstein, A., Pagnani, A., Huang, S. C., Chayes, J., Borgs, C., Zecchina, R., & Fraenkel, E. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2012.0092 · Cited by 114

Automated Prediction of Protein Association Rate Constants

Qin, S., Pang, X., & Zhou, H.-X. (2011) · Structure · doi:10.1016/j.str.2011.10.015 · Cited by 113

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

Meireles, L., Dömling, A. S. S., & Camacho, C. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq502 · Cited by 109

Architectures and Functional Coverage of Protein–Protein Interfaces

Tunçbağ, N., Gürsoy, A., Güney, E., Nussinov, R., & Keskin, Ö. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.071 · Cited by 109

PredUs: a web server for predicting protein interfaces using structural neighbors

Zhang, Q. C., Deng, L., Fisher, M., Guan, J., Honig, B. H., & Petrey, D. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr311 · Cited by 104

PINT: Protein-protein Interactions Thermodynamic Database

Kumar, M. D. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj017 · Cited by 103

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

Xu, Q., Canutescu, A. A., Wang, G., Shapovalov, M. V., Zoran Obradovic, A., & Dunbrack, R. L. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.06.002 · Cited by 102

HotRegion: a database of predicted hot spot clusters

Cukuroglu, E., Gürsoy, A., & Keskin, Ö. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr929 · Cited by 99

iAlign: a method for the structural comparison of protein–protein interfaces

Gao, M., & Skolnick, J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq404 · Cited by 98

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

Shulman‐Peleg, A., Shatsky, M., Nussinov, R., & Wolfson, H. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn185 · Cited by 97

PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

Phan, H. T. T., & Sternberg, M. J. E. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts119 · Cited by 94

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

Shoemaker, B. A., Zhang, D.-C., Tyagi, M., Thangudu, R. R., Fong, J. H., Marchler-Bauer, A., Bryant, S. H., Madej, T., & Panchenko, A. (2011) · Nucleic Acids Res. · doi:10.1093/nar/gkr997 · Cited by 89

PSIbase: a database of Protein Structural Interactome map (PSIMAP)

Gong, S., Yoon, G., Jang, I., Bolser, D. M., Dafas, P. A., Schroeder, M., Choi, H., Cho, Y., Han, K., Lee, S., et al. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti366 · Cited by 89

DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions

Bernauer, J., Bahadur, R. P., Rodier, F., Janin, J., & Anne Poupon, B. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn022 · Cited by 88

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms

Xu, Q., & Dunbrack, R. L. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1059 · Cited by 84

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

Assi, S. A., Tanaka, T. U., Rabbitts, T. H., & Fernández‐Fuentes, N. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1158 · Cited by 83

The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer

Acuner, S. E., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003470 · Cited by 80

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

Tunçbağ, N., Kar, G., Gürsoy, A., Keskin, Ö., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b905661k · Cited by 78

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

Tunçbağ, N., McCallum, S., Huang, S. C., & Fraenkel, E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks445 · Cited by 77

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

Cukuroglu, E., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086738 · Cited by 76

D OCKGROUND system of databases for protein recognition studies: Unbound structures for docking

Gao, Y. D., Douguet, D., Tovchigrechko, A., & Vakser, I. A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21714 · Cited by 76

SHARP2: protein–protein interaction predictions using patch analysis

Murakami, Y., & Jones, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl171 · Cited by 75

PredHS: a web server for predicting protein–protein interaction hot spots by using structural neighborhood properties

Deng, L., Zhang, Q. C., Chen, Z., Meng, Y., Guan, J., & Zhou, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku437 · Cited by 72

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference

Garcı́a-Garcı́a, J., Schleker, S., Klein‐Seetharaman, J., & Oliva, B. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks553 · Cited by 71

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

Chen, H., & Skolnick, J. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.114280 · Cited by 68

Constructing structural networks of signaling pathways on the proteome scale

Kuzu, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.04.004 · Cited by 64

Computational design of protein–protein interactions

Schreiber, G., & Fleishman, S. J. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.08.003 · Cited by 63

Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

Tunçbağ, N., Gürsoy, A., & Keskin, Ö. (2011) · Physical Biology · doi:10.1088/1478-3975/8/3/035006 · Cited by 63

Interactive proteomics research technologies: recent applications and advances

Petschnigg, J., Snider, J. D., & Štagljar, I. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.09.001 · Cited by 58

PiSite: a database of protein interaction sites using multiple binding states in the PDB

Higurashi, M., Ishida, T., & Kinoshita, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn659 · Cited by 58

Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces

Shazman, S., Celniker, G., Haber, O., Glaser, F., & Mandel‐Gutfreund, Y. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm401 · Cited by 58

iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein–Protein Interactions

Hosur, R., Xu, J., Bienkowska, J. R., & Berger, B. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.11.025 · Cited by 56

Human Proteome-scale Structural Modeling of E2–E3 Interactions Exploiting Interface Motifs

Kar, G., Keskin, Ö., Nussinov, R., & Gürsoy, A. (2011) · Journal of Proteome Research · doi:10.1021/pr2009143 · Cited by 55

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Miller, B. W., Lau, G., Grouios, C., Mollica, E., Barrios‐Rodiles, M., Liu, Y., Datti, A., Morris, Q., Wrana, J. L., & Attisano, L. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.72 · Cited by 55

Docking without docking: ISEARCH—prediction of interactions using known interfaces

Günther, S., May, P., Hoppe, A., Frömmel, C., & Preißner, R. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21746 · Cited by 53

HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

Fukuhara, N., & Kawabata, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn218 · Cited by 53

Predicting permanent and transient protein–protein interfaces

La, D., Kong, M., Hoffman, W., Choi, Y. I., & Kihara, D. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24235 · Cited by 53

KDBI: Kinetic Data of Bio-molecular Interactions database

Ji, Z. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg067 · Cited by 52

Prediction of protein–protein interactions between human host and a pathogen and its application to three pathogenic bacteria

Krishnadev, O., & Srinivasan, N. (2011) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2011.01.030 · Cited by 52

iLoops: a protein–protein interaction prediction server based on structural features

Planas-Iglesias, J., Marín-López, M. A., Bonet, J., Garcı́a-Garcı́a, J., & Oliva, B. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt401 · Cited by 47

Fast and accurate modeling of protein–protein interactions by combining template‐interface‐based docking with flexible refinement

Tunçbağ, N., Keskin, Ö., Nussinov, R., & Gürsoy, A. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24022 · Cited by 46

SCOWLP classification: Structural comparison and analysis of protein binding regions

Teyra, J., Paszkowski‐Rogacz, M., Anders, G., & Pisabarro, M. T. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-9 · Cited by 46

Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches

Sahu, S. S., Weirick, T., & Kaundal, R. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s11-s13 · Cited by 45

DIMA 3.0: Domain Interaction Map

Luo, Q., Pagel, P., Vilne, B., & Frishman, D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1200 · Cited by 45

Computational approaches for inferring the functions of intrinsically disordered proteins

Váradi, M., Vranken, W., Guharoy, M., & Tompa, P. (2015) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2015.00045 · Cited by 44

Evaluating template-based and template-free protein-protein complex structure prediction

Vreven, T., Hwang, H., Pierce, B. G., & Weng, Z. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt047 · Cited by 40

Integrating Structure to Protein-Protein Interaction Networks That Drive Metastasis to Brain and Lung in Breast Cancer

Engin, H. B., Güney, E., Keskin, Ö., Oliva, B., & Gürsoy, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081035 · Cited by 39

Alignment of Non-Covalent Interactions at Protein-Protein Interfaces

Zhu, H., Sommer, I., Lengauer, T., & Domingues, F. S. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001926 · Cited by 35

Artificial intelligence to deep learning: machine intelligence approach for drug discovery

Gupta, R., Srivastava, D., Sahu, M., Tiwari, S., Ambasta, R. K., & Kumar, P. (2021) · Molecular Diversity · doi:10.1007/s11030-021-10217-3 · Cited by 1,473

Deciphering molecular interactions by proximity labeling

Qin, W., Cho, K. F., Cavanagh, P. E., & Ting, A. Y. (2021) · Nature Methods · doi:10.1038/s41592-020-01010-5 · Cited by 671

Network-based prediction of protein interactions

Kovács, I. A., Luck, K., Spirohn, K., Wang, Y., Pollis, C., Schlabach, S., Bian, W., Kim, D., Kishore, N., Hao, T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09177-y · Cited by 480

Protein Assembly by Design

Zhu, J., Avakyan, N., Kakkis, A., Hoffnagle, A. M., Han, K., Li, Y., Zhang, Z., Choi, T. S., Na, Y., Yu, C.-J., et al. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00308 · Cited by 288

Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier

Chen, C., Zhang, Q., Yu, B., Yu, Z., Lawrence, P. J., Ma, Q., & Zhang, Y. (2020) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2020.103899 · Cited by 238

Computational Methods for Prediction of Protein-Protein Interactions

Rai, S., & Bhatnagar, S. (2016) · Advances in bioinformatics and biomedical engineering book series · doi:10.4018/978-1-5225-0427-6.ch010

Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction

Khatun, M. S., Shoombuatong, W., Hasan, M. M., & Kurata, H. (2020) · Current Genomics · doi:10.2174/1389202921999200625103936 · Cited by 34

Comparative Analysis of Computational Methods used in Protein-Protein Interaction (PPI) Studies

Ahuja, K., Joshi, A. A., Chakraborty, N., Purty, R. S., & Chatterjee, S. (2023) · River Publishers eBooks · doi:10.1201/9781003393238-4 · Cited by 2

Computational techniques for studying protein-protein interactions

Al-Khafaji, K., & Taşkın‐Tok, T. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90264-9.00009-x · Cited by 5

A survey on computational models for predicting protein–protein interactions

Hu, L., Wang, X., Huang, Y., Hu, P., & You, Z. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab036 · Cited by 189