Docking, scoring, and affinity prediction in CAPRI

Lensink, Marc F.; Wodak, Shoshana J.

doi:10.1002/prot.24428

Cited by 249Protein Structure and DynamicsComputational Drug Discovery MethodsEnzyme Structure and Function

Docking, scoring, and affinity prediction in CAPRI

Lensink, Marc F., Wodak, Shoshana J.·2013·Proteins Structure Function and Bioinformatics

DOI 10.1002/prot.24428

Open this paper in CoChat — free account

Abstract

We present the fifth evaluation of docking and related scoring methods used in the community-wide experiment on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation examined predictions submitted for a total of 15 targets in eight CAPRI rounds held during the years 2010-2012. The targets represented one the most diverse set tackled by the CAPRI community so far. They included only 10 "classical" docking and scoring problems. In one of the classical targets, the new challenge was to predict the position of water molecules in the protein-protein interface. The remaining five targets represented other new challenges that involved estimating the relative binding affinity and the effect of point mutations on the stability of designed and natural protein-protein complexes. Although the 10 classical CAPRI targets included two difficult multicomponent systems, and a protein-oligosaccharide complex with which CAPRI participants had little experience, this evaluation indicates that the performance of docking and scoring methods has remained quite robust. More remarkably, we find that automatic docking servers exhibit a significantly improved performance, with some servers now performing on par with predictions done by humans. The performance of CAPRI participants in the new challenges, briefly reviewed here, was mediocre overall, but some groups did relatively well and their approaches suggested ways of improving methods for designing binders and for estimating the free energies of protein assemblies, which should impact the field of protein modeling and design as a whole.

Integrity signals

Registry

Crossref · 10.1002/prot.24428

Cites

40 of 40 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

The six benchmark datasets have been widely used to test the predictive power of PPI prediction methods.
“These datasets have been widely used to test the predictive power of the PPI prediction methods [12, 13, 27–29, 29–35].”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [32]

Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066 · see citing works
Proteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,544 · see citing works
The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists
Alberts, B. (1998) · Cell · doi:10.1016/s0092-8674(00)80922-8 · Cited by 1,411 · see citing works
ModBase, a database of annotated comparative protein structure models, and associated resources
Pieper, U., Webb, B., Barkan, D. T., Schneidman‐Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E., Pettersen, E. F., Huang, C. C., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1091 · Cited by 1,069 · see citing works
A Census of Human Soluble Protein Complexes
Havugimana, P. C., Hart, T., Nepusz, T., Yang, H., Turinsky, A. L., Li, Z., Wang, P. I., Boutz, D. R., Fong, V., Phanse, S., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.011 · Cited by 843 · see citing works
Self-citation
A Protein Complex Network of Drosophila melanogaster
Guruharsha, K. G., Rual, J.-F. M., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C. N., Wong, C. S. F., Rhee, D. Y., Cenaj, O., et al. (2011) · Cell · doi:10.1016/j.cell.2011.08.047 · Cited by 654 · see citing works
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E.-M., Wilson, I. A., & Baker, D. (2011) · Science · doi:10.1126/science.1202617 · Cited by 585 · see citing works
High-resolution mapping of protein sequence-function relationships
Fowler, D. M., Araya, C. L., Fleishman, S. J., Kellogg, E. H., Stephany, J. J., Baker, D., & Fields, S. (2010) · Nature Methods · doi:10.1038/nmeth.1492 · Cited by 516 · see citing works
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 476 · see citing works
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 473 · see citing works
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
Mendez, R., Leplae, R., Maria, L. D., & Wodak, S. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10393 · Cited by 438 · see citing works
Self-citation
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000096 · Cited by 387 · see citing works
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
Whitehead, T. A., Chevalier, A. A., Song, Y., Dreyfus, C., Fleishman, S. J., de Mattos, C., Myers, C., Kamisetty, H., Blair, P. J., Wilson, I. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2214 · Cited by 364 · see citing works
Docking and scoring protein complexes: CAPRI 3rd Edition
Lensink, M., Mendez, R., & Wodak, S. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21804 · Cited by 351 · see citing works
Self-citation
Interrogating protein interaction networks through structural biology
Aloy, P., & Russell, R. B. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092147999 · Cited by 342 · see citing works
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
Méndez, R., Leplae, R., Lensink, M. F., & Wodak, S. J. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20551 · Cited by 340 · see citing works
Self-citation
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 · see citing works
Recent Progress and Future Directions in Protein-Protein Docking
Ritchie, D. W. (2008) · Current Protein and Peptide Science · doi:10.2174/138920308783565741 · Cited by 317 · see citing works
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
Babu, M., Vlasblom, J., Pu, S., Guo, X., Graham, C., Bean, B. D. M., Burston, H. E., Vizeacoumar, F. J., Snider, J. D., Phanse, S., et al. (2012) · Nature · doi:10.1038/nature11354 · Cited by 251 · see citing works
Self-citation
Integrative Structural Biology
Ward, A. B., Šali, A., & Wilson, I. A. (2013) · Science · doi:10.1126/science.1228565 · Cited by 239 · see citing works
Docking and scoring protein interactions: CAPRI 2009
Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226 · see citing works
Self-citation
Convergence and Combination of Methods in Protein-Protein Docking
Vajda, S., & Kozakov, D. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.02.008 · Cited by 221 · 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 basis of macromolecular recognition
Wodak, S. J., & Janin, J. (2002) · Advances in protein chemistry · doi:10.1016/s0065-3233(02)61001-0 · Cited by 172 · see citing works
Self-citation
Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes
Kühlmann, U. C., Pommer, A. J., Moore, G. R., James, R., & Kleanthous, C. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3945 · Cited by 154 · see citing works
Solvated docking: introducing water into the modelling of biomolecular complexes
van Dijk, A. D. J., & Bonvin, A. M. J. J. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl395 · Cited by 153 · see citing works
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
Fleishman, S. J., Whitehead, T. A., Strauch, E., Corn, J. E., Qin, S., Zhou, H., Mitchell, J. C., Demerdash, O., Takeda‐Shitaka, M., Terashi, G., et al. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.09.031 · Cited by 132 · see citing works
Self-citation
The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction
Meenan, N. A. G., Sharma, A. S., Fleishman, S. J., Macdonald, C., Morel, B., Boetzel, R., Moore, G. R., Baker, D. A., & Kleanthous, C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910756107 · Cited by 113 · see citing works
Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats
Urvoas, A., Guellouz, A., Valerio‐Lepiniec, M., Graille, M., Christiane, D. D., Desravines, D. C., TILBEURGH, H. V., Desmadril, M., & Minard, P. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.09.048 · Cited by 100 · see citing works
Structural consequences of effector protein complex formation in a diiron hydroxylase
Bailey, L. J., McCoy, J. G., Phillips, G. N., & Fox, B. G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807948105 · Cited by 99 · see citing works
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
Moretti, R., Fleishman, S. J., Agius, R., Torchala, M., Bates, P. A., Kastritis, P. L., Rodrigues, J., Trellet, M. E., Bonvin, A. M. J. J., Cui, M., et al. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24356 · Cited by 92 · see citing works
Self-citation
Trendspotting in the Protein Data Bank
Berman, H. M., Narayanan, B. C., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., Peisach, E., Prlić, A., Rose, P. W., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2012.12.029 · Cited by 82 · see citing works
Large Macromolecular Complexes in the Protein Data Bank: A Status Report
Dutta, S., & Berman, H. M. (2005) · Structure · doi:10.1016/j.str.2005.01.008 · Cited by 81 · see citing works
Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein
Liger, D., Mora, L., Lazar, N., Figaro, S., Henri, J., Scrima, N., Buckingham, R. H., TILBEURGH, H. V., Heurgué‐Hamard, V., & Graille, M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr176 · Cited by 81 · see citing works
Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep)
Guellouz, A., Valerio‐Lepiniec, M., Urvoas, A., Chevrel, A., Graille, M., Fourati, Z., Desmadril, M., TILBEURGH, H. V., & Minard, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071512 · Cited by 60 · see citing works
Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex
Wojdyla, J. A., Fleishman, S. J., Baker, D. A., & Kleanthous, C. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.01.019 · Cited by 56 · see citing works
Crystal structure of RlmA I : Implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site
Das, K., Acton, T., Chiang, Y., Shih, L., Arnold, E., & Montelione, G. T. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400189101 · Cited by 34 · see citing works
The targets of CAPRI Rounds 13–19
Janin, J. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22774 · Cited by 28 · see citing works
Structural basis of bacterial defense against g-type lysozyme-based innate immunity
Leysen, S., Vanderkelen, L., Weeks, S. D., Michiels, C. W., & Strelkov, S. V. (2012) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-1184-1 · Cited by 27 · see citing works
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions
Kundrotas, P. J., Zhu, Z., & Vakser, I. A. (2012) · Human Genomics · doi:10.1186/1479-7364-6-7 · Cited by 14 · see citing works

Flagged first, then by citations

Sorted by citations

The ClusPro web server for protein–protein docking
Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017) · Nature Protocols · doi:10.1038/nprot.2016.169 · Cited by 3,297 · see citing works
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.09.014 · Cited by 2,785 · see citing works
Software for molecular docking: a review
Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522 · see citing works
Coarse-Grained Protein Models and Their Applications
Kmiecik, S., Gront, D., Koliński, M., Wieteska, Ł., Badaczewska-Dawid, A. E., & Koliński, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00163 · Cited by 1,067 · see citing works
Performance and Its Limits in Rigid Body Protein-Protein Docking
Desta, I., Porter, K. A., Xia, B., Kozakov, D., & Vajda, S. (2020) · Structure · doi:10.1016/j.str.2020.06.006 · Cited by 697 · see citing works
Antibody Structure and Function: The Basis for Engineering Therapeutics
Chiu, M. L., Goulet, D. R., Teplyakov, A., & Gilliland, G. L. (2019) · Antibodies · doi:10.3390/antib8040055 · Cited by 646 · see citing works
New additions to the C lus P ro server motivated by CAPRI
Vajda, S., Yueh, C., Beglov, D., Bohnuud, T., Mottarella, S. E., Xia, B., Hall, D. R., & Kozakov, D. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25219 · Cited by 601 · see citing works
DockQ: A Quality Measure for Protein-Protein Docking Models
Basu, S., & Wallner, B. (2016) · PLOS ONE · doi:10.1371/journal.pone.0161879 · Cited by 460 · see citing works
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA
Baek, M., McHugh, R., Anishchenko, I., Jiang, H., Baker, D., & DiMaio, F. (2024) · Nature Methods · doi:10.1038/s41592-023-02086-5 · Cited by 372 · see citing works
Predicting Protein–Protein Interactions from the Molecular to the Proteome Level
Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369 · see citing works
Protein-Protein Docking: From Interaction to Interactome
Vakser, I. A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.08.033 · Cited by 318 · see citing works
GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
Lee, H., Heo, L., Lee, M. S., & Seok, C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv495 · Cited by 316 · see citing works
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
Yuriev, E., Holien, J. K., & Ramsland, P. A. (2015) · Journal of Molecular Recognition · doi:10.1002/jmr.2471 · Cited by 264 · see citing works
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI
Moult, J., Fidelis, K. A., Kryshtafovych, A., Schwede, T. F., & Tramontano, A. L. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25064 · Cited by 226 · see citing works
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
Lensink, M. F., Velankar, S., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25215 · Cited by 222 · see citing works
Self-citation
A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation
Wang, M., Cang, Z., & Wei, G.-W. (2020) · Nature Machine Intelligence · doi:10.1038/s42256-020-0149-6 · Cited by 202 · see citing works
Computational prediction of protein interfaces: A review of data driven methods
Xue, L. C., Dobbs, D. L., Bonvin, A. M. J. J., & Honavar, V. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.10.003 · Cited by 184 · see citing works
NMR approaches for structural analysis of multidomain proteins and complexes in solution
Göbl, C., Madl, T., Simon, B., & Sattler, M. (2014) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2014.05.003 · Cited by 175 · see citing works
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
Huang, S. (2014) · Drug Discovery Today · doi:10.1016/j.drudis.2014.02.005 · Cited by 164 · see citing works
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
Yan, Y., Wen, Z., Wang, X., & Huang, S. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25234 · Cited by 164 · see citing works
Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
Błaszczyk, M., Kurciński, M., Kouza, M., Wieteska, Ł., Dębiński, A., Koliński, A., & Kmiecik, S. (2015) · Methods · doi:10.1016/j.ymeth.2015.07.004 · Cited by 155 · see citing works
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
Lensink, M. F., Velankar, S. S., Kryshtafovych, A., Huang, S., Schneidman‐Duhovny, D., Šali, A., Segura, J., Fernández‐Fuentes, N., Viswanath, S., Elber, R., et al. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25007 · Cited by 153 · see citing works
Self-citation
BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts
Xiong, P., Zhang, C., Zheng, W., & Zhang, Y. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.11.022 · Cited by 140 · see citing works
Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
Liu, X., Luo, Y., Li, P., Song, S., & Peng, J. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009284 · Cited by 140 · see citing works
The structure assessment web server: for proteins, complexes and more
Waterhouse, A. M., Studer, G., Robin, X., Bienert, S., Tauriello, G., & Schwede, T. F. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae270 · Cited by 140 · see citing works
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT
Porter, K. A., Xia, B., Beglov, D., Bohnuud, T., Alam, N., Schueler‐Furman, O., & Kozakov, D. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx216 · Cited by 139 · see citing works
Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
Lensink, M. F., Nadzirin, N., Velankar, S. S., & Wodak, S. J. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25870 · Cited by 136 · see citing works
Self-citation
Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap
Jones, G. S., Jindal, A., Ghani, U., Kotelnikov, S., Egbert, M. E., Hashemi, N., Vajda, S., Padhorny, D., & Kozakov, D. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322002741 · Cited by 136 · see citing works
Progress and challenges in predicting protein interfaces
Esmaielbeiki, R., Krawczyk, K., Knapp, B., Nebel, J., & Deane, C. M. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv027 · Cited by 130 · see citing works
GRAMM Web Server for Protein Docking
Singh, A., Copeland, M. M., Kundrotas, P. J., & Vakser, I. A. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3441-7_5 · Cited by 132 · see citing works
Fully Blind Peptide-Protein Docking with pepATTRACT
Schindler, C., de Vries, S. J., & Zacharias, M. (2015) · Structure · doi:10.1016/j.str.2015.05.021 · Cited by 131 · see citing works
GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking
Heo, L., Lee, H., & Seok, C. (2016) · Scientific Reports · doi:10.1038/srep32153 · Cited by 125 · see citing works
Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment
Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25838 · Cited by 122 · see citing works
Self-citation
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning
Yin, R. M., Filho, H. V. R., Lin, V. C. L., Gowthaman, R., Cheung, M., & Pierce, B. G. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad356 · Cited by 110 · see citing works
Integrative computational modeling of protein interactions
Rodrigues, J., & Bonvin, A. M. J. J. (2014) · FEBS Journal · doi:10.1111/febs.12771 · Cited by 106 · see citing works
Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking
Huang, S. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.03.007 · Cited by 106 · see citing works
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
Lensink, M. F., Brysbaert, G., Mauri, T., Nadzirin, N., Velankar, S. S., Chaleil, R. A. G., Clarence, T., Bates, P. A., Kong, R., Liu, B., et al. (2021) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26222 · Cited by 105 · see citing works
Self-citation
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
Carlson, H. A., Smith, R. D., Damm‐Ganamet, K. L., Stuckey, J. A., Ahmed, A., Convery, M. A., Somers, D. O., Kranz, M., Elkins, P. A., Cui, G., et al. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00523 · Cited by 102 · see citing works
A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT
de Vries, S. J., Schindler, C., de Beauchêne, I. C., & Zacharias, M. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.12.015 · Cited by 100 · see citing works
Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data
Hufsky, F., & Böcker, S. (2016) · Mass Spectrometry Reviews · doi:10.1002/mas.21489 · Cited by 100 · see citing works
Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?
Geng, C., Xue, L. C., Roel‐Touris, J., & Bonvin, A. M. J. J. (2019) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1410 · Cited by 100 · see citing works
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
Saladin, A., Rey, J., Thévenet, P., Zacharias, M., Moroy, G., & Tufféry, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku404 · Cited by 97 · see citing works
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots
Sukhwal, A., & Sowdhamini, R. (2015) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s25928 · Cited by 96 · see citing works
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment
Lensink, M. F., Velankar, S. S., Baek, M., Heo, L., Seok, C., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25419 · Cited by 95 · see citing works
Self-citation
Integrative Modelling of Biomolecular Complexes
Koukos, P. I., & Bonvin, A. M. J. J. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.009 · Cited by 89 · see citing works
Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era
dos Santos-Silva, C. A., Zupin, L., Oliveira-Lima, M., Vilela, L. M. B., Bezerra-Neto, J. P., Ferreira‐Neto, J. R. C., Ferreira, J. D. C., Silva, R. L. D. O., Pires, C. D. J., Aburjaile, F. F., et al. (2020) · Bioinformatics and Biology Insights · doi:10.1177/1177932220952739 · Cited by 84 · see citing works
pyDockSAXS: protein–protein complex structure by SAXS and computational docking
Jiménez‐García, B., Pons, C., Svergun, D. I., Bernadó, P., & Fernández‐Recio, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv368 · Cited by 74 · see citing works
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
Wodak, S. J., Vajda, S., Lensink, M. F., Kozakov, D., & Bates, P. A. (2023) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-102622-084607 · Cited by 71 · see citing works
Self-citation
Score_set: A CAPRI benchmark for scoring protein complexes
Lensink, M. F., & Wodak, S. J. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24678 · Cited by 71 · see citing works
Self-citation
iScore: a novel graph kernel-based function for scoring protein–protein docking models
Geng, C., Jung, Y. G., Renaud, N., Honavar, V., Bonvin, A. M. J. J., & Xue, L. C. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz496 · Cited by 71 · see citing works
Docking Server for the Identification of Heparin Binding Sites on Proteins
Mottarella, S. E., Beglov, D., Beglova, N., Nugent, M. A., Kozakov, D., & Vajda, S. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci500115j · Cited by 70 · see citing works
An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles
Sudha, G., Nussinov, R., & Srinivasan, N. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.004 · Cited by 69 · see citing works
Protein–Protein and Protein–Peptide Docking with ClusPro Server
Alekseenko, A. E., Ignatov, M., Jones, G. S., Sabitova, M., & Kozakov, D. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0708-4_9 · Cited by 68 · see citing works
Challenges in structural approaches to cell modeling
Im, W., Liang, J., Olson, A. J., Zhou, H., Vajda, S., & Vakser, I. A. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.05.024 · Cited by 66 · see citing works
iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement
Schindler, C., de Vries, S. J., & Zacharias, M. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24728 · Cited by 65 · see citing works
Evolution of protein interactions: From interactomes to interfaces
Andréani, J., & Guérois, R. (2014) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2014.05.010 · Cited by 64 · see citing works
In silico methods for design of biological therapeutics
Roy, A., Nair, S. A., Sen, N., Soni, N., & Madhusudhan, M. S. (2017) · Methods · doi:10.1016/j.ymeth.2017.09.008 · Cited by 62 · see citing works
Encounter complexes and dimensionality reduction in protein–protein association
Kozakov, D., Li, K., Hall, D. R., Beglov, D., Zheng, J., Vakili, P., Schueler‐Furman, O., Paschalidis, I. C., Clore, G. M., & Vajda, S. (2014) · eLife · doi:10.7554/elife.01370 · Cited by 60 · see citing works
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes
Jensen, K. K., Rantos, V., Jappe, E. C., Olsen, T. H., Jespersen, M. C., Jurtz, V. I., Jessen, L. E., Lanzarotti, E., Mahajan, S., Peters, B., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-50932-4 · Cited by 59 · see citing works
CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications
Steinmetz, A. C. U., Vallée, F., Beil, C., Lange, C. M., Baurin, N., Beninga, J., Capdevila, C., Corvey, C., Dupuy, A., Ferrari, P., et al. (2016) · mAbs · doi:10.1080/19420862.2016.1162932 · Cited by 59 · see citing works
Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Complexes with HADDOCK”
van Zundert, G. C. P., & Bonvin, A. M. J. J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0366-5_12 · Cited by 58 · see citing works
Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry
Bullock, J. M. A., Sen, N., Thalassinos, K., & Topf, M. (2018) · Structure · doi:10.1016/j.str.2018.04.016 · Cited by 58 · see citing works
Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design
Cannon, D. A., Shan, L., Du, Q., Shirinian, L., Rickert, K. W., Rosenthal, K. L., Korade, M., van Vlerken-Ysla, L. E., Buchanan, A. G., Vaughan, T. J., et al. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006980 · Cited by 54 · see citing works
Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK
Geng, C., Narasimhan, S., Rodrigues, J., & Bonvin, A. M. J. J. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6798-8_8 · Cited by 52 · see citing works
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
Jandová, Z., Vargiu, A. V., & Bonvin, A. M. J. J. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00336 · Cited by 52 · see citing works
Protein–Protein Docking: Past, Present, and Future
Sunny, S., & Jayaraj, P. B. (2021) · The Protein Journal · doi:10.1007/s10930-021-10031-8 · Cited by 50 · see citing works
Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes
Mirabello, C., Wallner, B., Nystedt, B., Azinas, S., & Carroni, M. (2024) · Nature Communications · doi:10.1038/s41467-024-52951-w · Cited by 50 · see citing works
Computational modeling of protein assemblies
Soni, N., & Madhusudhan, M. S. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.04.006 · Cited by 50 · see citing works
Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes
Nithin, C., Ghosh, P., & Bujnicki, J. M. (2018) · Genes · doi:10.3390/genes9090432 · Cited by 48 · see citing works
Accounting for pairwise distance restraints in FFT-based protein–protein docking
Xia, B., Vajda, S., & Kozakov, D. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw306 · Cited by 47 · see citing works
InterPep2: global peptide–protein docking using interaction surface templates
Johansson-Åkhe, I., Mirabello, C., & Wallner, B. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa005 · Cited by 47 · see citing works
CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking
Kong, R., Wang, F., Zhang, J., Wang, F., & Chang, S. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00445 · Cited by 46 · see citing works
Predicting peptide binding sites on protein surfaces by clustering chemical interactions
Yan, C., & Zou, X. (2014) · Journal of Computational Chemistry · doi:10.1002/jcc.23771 · Cited by 45 · see citing works
High-resolution protein–protein docking by global optimization: recent advances and future challenges
Park, H., Lee, H., & Seok, C. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.08.001 · Cited by 44 · see citing works
Pushing the Backbone in Protein-Protein Docking
Kuroda, D., & Gray, J. J. (2016) · Structure · doi:10.1016/j.str.2016.06.025 · Cited by 44 · see citing works
CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes
Collins, K. W., Copeland, M. M., Brysbaert, G., Wodak, S. J., Bonvin, A. M. J. J., Kundrotas, P. J., Vakser, I. A., & Lensink, M. F. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168540 · Cited by 42 · see citing works
Self-citation
Template-Based Modeling of Protein-RNA Interactions
Zheng, J., Kundrotas, P. J., Vakser, I. A., & Liu, S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005120 · Cited by 42 · see citing works
PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets
Yu, J., & Guérois, R. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw533 · Cited by 41 · see citing works
Application of docking methodologies to modeled proteins
Singh, A., Dauzhenka, T. A., Kundrotas, P. J., Sternberg, M. J. E., & Vakser, I. A. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25889 · Cited by 41 · see citing works
Lessons from (co‐)evolution in the docking of proteins and peptides for CAPRI Rounds 28–35
Yu, J., Andréani, J., Ochsenbein, F., & Guérois, R. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25180 · Cited by 40 · see citing works
From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations
Schwierz, N., Frost, C. V., Geissler, P. L., & Zacharias, M. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b10189 · Cited by 39 · see citing works
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification
Elez, K., Bonvin, A. M. J. J., & Vangone, A. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2414-9 · Cited by 38 · see citing works
CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
Chermak, E., Petta, A., Serra, L., Vangone, A., Scarano, V., Cavallo, L., & Oliva, R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu837 · Cited by 38 · see citing works
Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities
Guilhot-Gaudeffroy, A., Froidevaux, C., Azé, J., & Bernauer, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108928 · Cited by 36 · see citing works
Improved Antibody‐Specific Epitope Prediction Using AlphaFold and AbAdapt**
(2022) · doi:10.1002/cbic.202200303 · Cited by 36 · see citing works
Critical Assessment of Protein Cross-Linking and Molecular Docking: An Updated Model for the Interaction Between Photosystem II and Psb27
Cormann, K. U., Möller, M., & Nowaczyk, M. M. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00157 · Cited by 34 · see citing works
Protein complex analysis: From raw protein lists to protein interaction networks
Meysman, P., Titeca, K., Eyckerman, S., Tavernier, J. H., Goethals, B., Martens, L., Valkenborg, D., & Laukens, K. (2015) · Mass Spectrometry Reviews · doi:10.1002/mas.21485 · Cited by 33 · see citing works
A benchmark testing ground for integrating homology modeling and protein docking
Bohnuud, T., Luo, L., Wodak, S. J., Bonvin, A. M. J. J., Weng, Z., Vajda, S., Schueler‐Furman, O., & Kozakov, D. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25063 · Cited by 33 · see citing works
Self-citation
Protein–protein interaction specificity is captured by contact preferences and interface composition
Nadalin, F., & Carbone, A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx584 · Cited by 33 · see citing works
Protein–Protein Docking in Drug Design and Discovery
Kaczor, A. A., Bartuzi, D., Stępniewski, T. M., Matosiuk, D., & Selent, J. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7756-7_15 · Cited by 33 · see citing works
Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking
Pereira, G. P., Jiménez‐García, B., Pellarin, R., Launay, G., Wu, S., Martin, J., & Souza, P. C. T. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01154 · Cited by 32 · see citing works
Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models
Chermak, E., Donato, R. D., Lensink, M. F., Petta, A., Serra, L., Scarano, V., Cavallo, L., & Oliva, R. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166460 · Cited by 31 · see citing works
Self-citation
Molecular Modeling Applied to Nucleic Acid-Based Molecule Development
Krüger, A., Zimbres, F. M., Kronenberger, T., & Wrenger, C. (2018) · Biomolecules · doi:10.3390/biom8030083 · Cited by 31 · see citing works
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
Krupa, P., Karczyńska, A. S., Mozolewska, M. A., Liwo, A., & Czaplewski, C. R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa897 · Cited by 30 · see citing works
AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence
Davila, A., Xu, Z., Li, S., Rozewicki, J., Wilamowski, J., Kotelnikov, S., Kozakov, D., Teraguchi, S., & Standley, D. M. (2022) · Bioinformatics Advances · doi:10.1093/bioadv/vbac015 · Cited by 30 · see citing works
Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro
Xia, B., Mamonov, A. B., Leysen, S., Allen, K. N., Strelkov, S. V., Paschalidis, I. C., Vajda, S., & Kozakov, D. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.23952 · Cited by 29 · see citing works
Prediction and redesign of protein–protein interactions
Lua, R. C., Marciano, D. C., Katsonis, P., Adikesavan, A. K., Wilkins, A. D., & Lichtarge, O. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.05.004 · Cited by 28 · see citing works
Information-Driven Modeling of Protein-Peptide Complexes
Trellet, M. E., Melquiond, A. S. J., & Bonvin, A. M. J. J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-2285-7_10 · Cited by 28 · see citing works
FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility
Marcu, O., Dodson, E. J., Alam, N., Sperber, M., Kozakov, D., Lensink, M. F., & Schueler‐Furman, O. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25230 · Cited by 27 · see citing works
Self-citation
DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes
Viswanath, S., Ravikant, D. V. S., & Elber, R. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0366-5_14 · Cited by 26 · see citing works

Docking and scoring protein interactions: CAPRI 2009
Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226 · see citing works
Self-citation
Score_set: A CAPRI benchmark for scoring protein complexes
Lensink, M. F., & Wodak, S. J. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24678 · Cited by 71 · see citing works
Self-citation
Docking and scoring protein complexes: CAPRI 3rd Edition
Lensink, M., Mendez, R., & Wodak, S. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21804 · Cited by 351 · see citing works
Self-citation
Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment
Janin, J. (2012) · Focus on structural biology · doi:10.1007/978-94-007-5285-6_5 · Cited by 5 · see citing works
CAPRI: A Critical Assessment of PRedicted Interactions
Wodak, S. J. (2014)
Self-citation

Authors: Lensink, M. F., & Wodak, S. J.
Affiliations: Centre National de la Recherche Scientifique (FR)
University of Toronto (CA)
Corresponding author: Lensink, Marc F.
ORCID: Lensink, Marc F.
Wodak, Shoshana J.
Venue: Proteins Structure Function and Bioinformatics
Publisher: Wiley
Published: 2013-10-17
Volume: 81
Issue: 12
Pages: 2082-2095
ISSN: 0887-3585 (ISSN-L)
1097-0134
DOI: 10.1002/prot.24428
OpenAlex: W2165531467
Cited by: 249
References: 40
Citations by year: 2026: 7 · 2025: 11 · 2024: 11 · 2023: 15 · 2022: 11 · 2021: 9 · 2020: 18 · 2019: 21 · 2018: 21 · 2017: 22 · 2016: 46 · 2015: 27 · 2014: 27 · 2013: 1
FWCI: 15.07
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Proteins Structure Function and Bioinformatics (publishedVersion)
PubMed (publishedVersion)
HAL (submittedVersion)
Funders: French Agence Nationale de Recherche (ANR-12-BSV5-0009-01 (to M.F.L.))
Canada Institute of Health Research, Sickkids Foundation, Ontario Research Fund, PrioNet Network of Excellence, Canada
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: protein-protein docking, docking scoring functions, binding affinity prediction, free energy calculation
MeSH terms: Humans, Ligands, Protein Binding, Protein Conformation, Proteins, Software, Water, Computational Biology, Protein Interaction Mapping, Molecular Docking Simulation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Docking, scoring, and affinity prediction in CAPRI

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks