The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Templates are available to model nearly all complexes of structurally characterized proteins
Open accessAbstract
Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides the possibility of aligning the structures of the proteins and the template complexes. The progress in the development of template-based docking and the vast experience in template-based modeling of individual proteins show that, generally, such approaches are more reliable than the free modeling. The key aspect of this modeling paradigm is the availability of the templates. The current common perception is that due to the difficulties in experimental structure determination of protein-protein complexes, the pool of docking templates is insignificant, and thus a broad application of template-based docking is possible only at some future time. The results of our large scale, systematic study show that, surprisingly, in spite of the limited number of protein-protein complexes in the Protein Data Bank, docking templates can be found for complexes representing almost all the known protein-protein interactions, provided the components themselves have a known structure or can be homology-built. About one-third of the templates are of good quality when they are compared to experimental structures in test sets extracted from the Protein Data Bank and would be useful starting points in modeling the complexes. This finding dramatically expands our ability to model protein interactions, and has far-reaching implications for the protein docking field in general.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
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?
In the citing paper
“The rise of the comparative modeling of protein-protein complexes (template-based docking), based on the rapid expansion of PDB, makes the availability of templates for docking procedures routine [12,13].”
From Challenges in protein docking (2020) · cites this paper as [12]
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
TM-align: a protein structure alignment algorithm based on the TM-score
Zhang, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki524 · Cited by 3,774
The Database of Interacting Proteins: 2004 update
Salwinski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh086 · Cited by 2,271
An improved algorithm for matching biological sequences
Gotoh, O. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90398-9 · Cited by 1,726
PIPER: An FFT‐based protein docking program with pairwise potentials
Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21117 · Cited by 865
CAPRI: A Critical Assessment of PRedicted Interactions
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703
Critical assessment of methods of protein structure prediction (CASP) — round x
Moult, J., Fidelis, K. A., Kryshtafovych, A., Schwede, T. F., & Tramontano, A. L. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24452 · Cited by 687
The Biomolecular Interaction Network Database and related tools 2005 update
Alfarano, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki051 · Cited by 587
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
de Vries, S. J., van Dijk, A. D. J., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V. L., Wassenaar, T. A., & Bonvin, A. M. J. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21723 · Cited by 555
Cited by
Sorted by citations
SWISS-MODEL: homology modelling of protein structures and complexes
Waterhouse, A. M., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T., Rempfer, C., Bordoli, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky427 · Cited by 13,248
Improved prediction of protein-protein interactions using AlphaFold2
Bryant, P., Pozzati, G., & Elofsson, A. (2021) · doi:10.1101/2021.09.15.460468 · Cited by 1,022
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017) · Scientific Reports · doi:10.1038/s41598-017-09654-8 · Cited by 791
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
Structure, Dynamics, Assembly, and Evolution of Protein Complexes
Marsh, J. A., & Teichmann, S. A. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034142 · Cited by 473
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
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
Yin, R., Feng, B. Y., Varshney, A., & Pierce, B. G. (2022) · Protein Science · doi:10.1002/pro.4379 · Cited by 335
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
Yin, R., Feng, B. Y., Varshney, A., & Pierce, B. G. (2021) · doi:10.1101/2021.10.23.465575 · Cited by 335
Protein-Protein Docking: From Interaction to Interactome
Vakser, I. A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.08.033 · Cited by 318
Protein-peptide docking: opportunities and challenges
Ciemny, M., Kurcinski, M., Kamel, K., Kolinski, A., Alam, N., Schueler-Furman, O., & Kmiecik, S. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.05.006 · Cited by 306
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
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
Protein–protein interaction prediction with deep learning: A comprehensive review
Soleymani, F., Paquet, E., Viktor, H. L., Michalowski, W., & Spinello, D. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.08.070 · Cited by 209
Computational prediction of protein–protein binding affinities
Siebenmorgen, T., & Zacharias, M. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1448 · Cited by 184
“36 Hence, many interactions especially those mediated by reoccurring protein domains can be modeled based on similarity to an already known interaction.”
BackgroundTemplate-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
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
Yan, Y., Wen, Z., Wang, X., & Huang, S. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25234 · Cited by 164
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
Othman, H., Bouslama, Z., Brandenburg, J., da Rocha, J., Hamdi, Y., Ghedira, K., Srairi‐Abid, N., & Hazelhurst, S. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.05.028 · Cited by 144
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 137
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 138
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
Protein Modeling: What Happened to the “Protein Structure Gap”?
Schwede, T. F. (2013) · Structure · doi:10.1016/j.str.2013.08.007 · Cited by 128
Heo, L., Lee, H., & Seok, C. (2016) · Scientific Reports · doi:10.1038/srep32153 · Cited by 125
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
Self-citationWhat method to use for protein–protein docking?
Porter, K. A., Desta, I., Kozakov, D., & Vajda, S. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.12.010 · Cited by 119
Villoutreix, B. O., Kuenemann, M. A., Poyet, J., Bruzzoni‐Giovanelli, H., Labbé, C. M., Lagorce, D., Spérandio, O., & Miteva, M. A. (2014) · Molecular Informatics · doi:10.1002/minf.201400040 · Cited by 118
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 106
Integrative computational modeling of protein interactions
Rodrigues, J., & Bonvin, A. M. J. J. (2014) · FEBS Journal · doi:10.1111/febs.12771 · Cited by 106
An integration of deep learning with feature embedding for protein–protein interaction prediction
Yao, Y., Du, X., Diao, Y., & Zhu, H. (2019) · PeerJ · doi:10.7717/peerj.7126 · Cited by 108
Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments
Grassmann, G., Miotto, M., Desantis, F., Rienzo, L. D., Tartaglia, G. G., Pastore, A., Ruocco, G., Monti, M. M., & Milanetti, E. (2024) · Chemical Reviews · doi:10.1021/acs.chemrev.3c00550 · Cited by 109
Hashemi, Z. S., Zarei, M., Fath, M. K., Ganji, M., Farahani, M. S., Afsharnouri, F., Pourzardosht, N., Khalesi, B., Jahangiri, A., Rahbar, M. R., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.669431 · Cited by 105
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 97
Towards a detailed atlas of protein–protein interactions
Mosca, R., Pons, T., Ceol, A. G. M., Valencia, A., & Aloy, P. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.07.005 · Cited by 91
Andréani, J., Faure, G., & Guérois, R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt260 · Cited by 84
Dockground: A comprehensive data resource for modeling of protein complexes
Kundrotas, P. J., Anishchenko, I. V., Dauzhenka, T. A., Kotthoff, I., Mnevets, D., Copeland, M. M., & Vakser, I. A. (2017) · Protein Science · doi:10.1002/pro.3295 · Cited by 82
An overview of in silico vaccine design against different pathogens and cancer
Kardani, K., Bolhassani, A., & Namvar, A. (2020) · Expert Review of Vaccines · doi:10.1080/14760584.2020.1794832 · Cited by 85
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
Predicting protein-peptide interaction sites using distant protein complexes as structural templates
Johansson-Åkhe, I., Mirabello, C., & Wallner, B. (2019) · Scientific Reports · doi:10.1038/s41598-019-38498-7 · Cited by 71
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 73
Sudha, G., Nussinov, R., & Srinivasan, N. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.004 · Cited by 70
Schindler, C., de Vries, S. J., & Zacharias, M. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24728 · Cited by 65
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 70
TCRmodel: high resolution modeling of T cell receptors from sequence
Gowthaman, R., & Pierce, B. G. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky432 · Cited by 60
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 70
Vakser, I. A. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.07.001 · Cited by 62
Defining the limits of homology modeling in information‐driven protein docking
Rodrigues, J., Melquiond, A. S. J., Karaca, E., Trellet, M. E., van Dijk, M., van Zundert, G. C. P., Schmitz, C., de Vries, S. J., Bordogna, A., Bonati, L., et al. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24382 · Cited by 63
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
Algorithmic approaches to protein-protein interaction site prediction
Aumentado‐Armstrong, T., Istrate, B., & Murgita, R. A. (2015) · Algorithms for Molecular Biology · doi:10.1186/s13015-015-0033-9 · Cited by 63
Structural Bioinformatics of the Interactome
Petrey, D. S., & Honig, B. H. (2014) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-051013-022726 · Cited by 61
Exploring protein-protein interactions at the proteome level
Elhabashy, H., Merino, F., Alva, V., Kohlbacher, O., & Lupas, A. N. (2022) · Structure · doi:10.1016/j.str.2022.02.004 · Cited by 57
Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry
Guven‐Maiorov, E., Tsai, C., & Nussinov, R. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.01236 · Cited by 64
Molecular Modelling in Bioactive Peptide Discovery and Characterisation
Agoni, C., Fernández-Díaz, R., Timmons, P. B., Adelfio, A., Gómez, H., & Shields, D. C. (2025) · Biomolecules · doi:10.3390/biom15040524 · Cited by 63
Assessment of ligand binding site predictions in CASP10
Cassarino, T. G., Bordoli, L., & Schwede, T. (2014) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24495 · Cited by 42
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
Structural host-microbiota interaction networks
Guven‐Maiorov, E., Tsai, C., & Nussinov, R. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005579 · Cited by 55
Tonolo, F., Grinzato, A., Bindoli, A., & Rigobello, M. P. (2023) · Antioxidants · doi:10.3390/antiox12030665 · Cited by 50
Nithin, C., Ghosh, P., & Bujnicki, J. M. (2018) · Genes · doi:10.3390/genes9090432 · Cited by 48
Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale
Kuzu, G., Gursoy, A., Nussinov, R., & Keskin, O. (2013) · Journal of Proteome Research · doi:10.1021/pr400006k · Cited by 47
Template-based prediction of protein function
Petrey, D. S., Chen, T. S., Deng, L., Garzón, J. I., Hwang, H., Lasso, G., Lee, H., Silkov, A., & Honig, B. H. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.01.007 · Cited by 48
Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development
Duran‐Frigola, M., Mosca, R., & Aloy, P. (2013) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.03.004 · Cited by 44
HOMCOS: an updated server to search and model complex 3D structures
Kawabata, T. (2016) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-016-9208-y · Cited by 45
Park, H., Lee, H., & Seok, C. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.08.001 · Cited by 44
Understanding Protein–Protein Interactions Using Local Structural Features
Planas-Iglesias, J., Bonet, J., Garcı́a-Garcı́a, J., Marín-López, M. A., Feliu, E., & Oliva, B. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.01.014 · Cited by 44
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
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
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
Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver
Yan, Y., & Huang, S. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0708-4_12 · Cited by 40
Kundrotas, P. J., & Vakser, I. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24392 · Cited by 37
Rodriguez-Rivas, J., Marsili, S., Juan, D., & Valencia, A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1611861114 · Cited by 36
Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone
Negroni, J., Mosca, R., & Aloy, P. (2014) · Structure · doi:10.1016/j.str.2014.07.009 · Cited by 35
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
P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking
Zheng, J., Hong, X., Xie, J., Tong, X., & Liu, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz478 · Cited by 31
Quignot, C., Postic, G., Bret, H., Rey, J., Granger, P., Murail, S., Chacón, P., Andréani, J., Tufféry, P., & Guérois, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab358 · Cited by 34
Design and designability of protein-based assemblies
Zhang, J., Zheng, F., & Grigoryan, G. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.05.009 · Cited by 30
Docking approaches for modeling multi-molecular assemblies
Rosell, M., & Fernández‐Recio, J. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.05.016 · Cited by 28
Si, D., Nakamura, A., Tang, R., Guan, H., Hou, J., Firozi, A., Cao, R., Hippe, K., & Zhao, M. (2021) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1542 · Cited by 32
Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
Sikosek, T., Krobath, H., & Chan, H. S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004960 · Cited by 30
Guven‐Maiorov, E., Tsai, C., Ma, B., & Nussinov, R. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.10.023 · Cited by 31
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 29
Modeling complexes of modeled proteins
Anishchenko, I. V., Kundrotas, P. J., & Vakser, I. A. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25183 · Cited by 26
Structural templates for comparative protein docking
Anishchenko, I. V., Kundrotas, P. J., Tuzikov, A. V., & Vakser, I. A. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24736 · Cited by 26
Toward a three-dimensional view of protein networks between species
Franzosa, E. A., Garamszegi, S., & Xia, Y. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00428 · Cited by 26
Specificity and stability of transient protein–protein interactions
Vishwanath, S., Sukhwal, A., Sowdhamini, R., & Srinivasan, N. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.12.010 · Cited by 27
Limits and potential of combined folding and docking
Pozzati, G., Zhu, W., Bassot, C., Lamb, J., Kundrotas, P., & Elofsson, A. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btab760 · Cited by 25
Self-citationMuratcioğlu, S., Guven‐Maiorov, E., Keskin, Ö., & Gürsoy, A. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.10.001 · Cited by 26
Protein–protein interaction networks studies and importance of 3D structure knowledge
Lu, H., Fornili, A., & Fraternali, F. (2013) · Expert Review of Proteomics · doi:10.1586/14789450.2013.856764 · Cited by 25
Dockground resource for protein recognition studies
Collins, K. W., Copeland, M. M., Kotthoff, I., Singh, A., Kundrotas, P. J., & Vakser, I. A. (2022) · Protein Science · doi:10.1002/pro.4481 · Cited by 22
Protein models: The Grand Challenge of protein docking
Anishchenko, I. V., Kundrotas, P. J., Tuzikov, A. V., & Vakser, I. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24385 · Cited by 23
Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems
Barradas‐Bautista, D., Rosell, M., Pallara, C., & Fernández‐Recio, J. (2017) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2017.06.003 · Cited by 24
Text Mining for Protein Docking
Badal, V. D., Kundrotas, P. J., & Vakser, I. A. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004630 · Cited by 22
Structural Basis of Protein–Protein Interactions
Liddington, R. (2004) · Humana Press eBooks · doi:10.1385/1-59259-762-9:003 · Cited by 22
Interface-Based Structural Prediction of Novel Host-Pathogen Interactions
Guven‐Maiorov, E., Tsai, C., Ma, B., & Nussinov, R. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8736-8_18 · Cited by 21
Kilambi, K. P., Pacella, M. S., Xu, J., Labonte, J. W., Porter, J. R., Muthu, P., Drew, K., Kuroda, D., Schueler‐Furman, O., Bonneau, R., et al. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24425 · Cited by 20
Non-interacting proteins may resemble interacting proteins: prevalence and implications
Launay, G., Ceres, N., & Martin, J. (2017) · Scientific Reports · doi:10.1038/srep40419 · Cited by 20
Kundrotas, P. J., Anishchenko, I. V., Badal, V. D., Das, M., Dauzhenka, T. A., & Vakser, I. A. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25380 · Cited by 20
Integrating ab initio and template-based algorithms for protein–protein complex structure prediction
Vangaveti, S., Vreven, T., Zhang, Y., & Weng, Z. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz623 · Cited by 20
Metadata
- Authors
- Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A.
- Affiliations
- University of Kansas (US)
- University of California San Diego (US)
- Université Paris-Sud (FR)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-05-29
- Volume
- 109
- Issue
- 24
- Pages
- 9438-9441
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3386081
- OpenAlex
- W2163614321
- Cited by
- 179
- References
- 34
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 3 · 2023: 7 · 2022: 16 · 2021: 11 · 2020: 18 · 2019: 14 · 2018: 12 · 2017: 16 · 2016: 22 · 2015: 9 · 2014: 18 · 2013: 20 · 2012: 3
- FWCI
- 6.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM074255)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- template-based docking, protein-protein docking, protein-protein complex, Protein Data Bank, protein-protein interaction, homology modeling, structural alignment
- MeSH terms
- Models, Molecular, Proteins, Databases, Protein
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
