PatchDock and SymmDock: servers for rigid and symmetric docking
Open accessAbstract
Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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 most robust results for docking stable scaffolds against the target structure RIF were obtained using direct low-resolution shape matching followed by grid-based refinement of the rigid body orientation in the RIF (RIFDock).
“The most robust results were obtained using direct low-resolution shape matching11 followed by grid-based refinement of the rigid body orientation in the RIF (RIFDock).”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [11]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763 · see citing works
Solvent-Accessible Surfaces of Proteins and Nucleic Acids
Connolly, M. L. (1983) · Science · doi:10.1126/science.6879170 · Cited by 2,759 · see citing works
Analytical molecular surface calculation
Connolly, M. L. (1983) · Journal of Applied Crystallography · doi:10.1107/s0021889883010985 · Cited by 2,536 · see citing works
A geometric approach to macromolecule-ligand interactions
Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90153-x · Cited by 2,287 · see citing works
Shape complementarity at protein–protein interfaces
Norel, R., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1994) · Biopolymers · doi:10.1002/bip.360340711 · Cited by 1,208 · see citing works
Self-citationKatchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A., Aflalo, C., & Vakser, I. (1992) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.89.6.2195 · Cited by 1,143 · see citing works
Gray, J. J., Moughon, S. E., Wang, C., Schueler‐Furman, O., Kuhlman, B. A., Rohl, C. A., & Baker, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00670-3 · Cited by 1,130 · see citing works
ClusPro: a fully automated algorithm for protein-protein docking
Comeau, S. R., GATCHELL, D. W., Vajda, S., & Camacho, C. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh354 · Cited by 826 · see citing works
Gabb, H. A., Jackson, R. M., & Sternberg, M. J. E. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1203 · Cited by 820 · see citing works
Cuff, J. A., & Barton, G. J. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20000815)40:3 · Cited by 768 · see citing works
Efficient Unbound Docking of Rigid Molecules
Duhovny, D., Nussinov, R., & Wolfson, H. J. (2002) · Lecture notes in computer science · doi:10.1007/3-540-45784-4_14 · Cited by 729 · see citing works
Self-citationDetermination of atomic desolvation energies from the structures of crystallized proteins
Zhang, C., Vasmatzis, G., Cornette, J. L., & DeLisi, C. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0859 · Cited by 536 · see citing works
“Soft docking”: Matching of molecular surface cubes
Jiang, F., & Kim, S. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90859-5 · Cited by 407 · see citing works
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
Chen, R., & Weng, Z. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10092 · Cited by 375 · see citing works
A protein–protein docking benchmark
Chen, R., Mintseris, J., Janin, J., & Weng, Z. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10390 · Cited by 345 · see citing works
Development and Validation of a Genetic Algorithm for Flexible Docking
rWillett, P. (1997) · Cited by 306 · see citing works
Protein docking for low-resolution structures
Vakser, I. A. (1995) · Protein Engineering Design and Selection · doi:10.1093/protein/8.4.371 · Cited by 246 · see citing works
Geometry‐based flexible and symmetric protein docking
Schneidman‐Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20562 · Cited by 203 · see citing works
Self-citationShape complementarity at the hemoglobin α1β1 subunit interface
Connolly, M. L. (1986) · Biopolymers · doi:10.1002/bip.360250705 · Cited by 200 · see citing works
A geometry-based suite of moleculardocking processes
Fischer, D., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(95)80063-8 · Cited by 188 · see citing works
Self-citationA systematic study of low-resolution recognition in protein-protein complexes
Vakser, I. A., Matar, O. G., & Lam, C. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.15.8477 · Cited by 180 · see citing works
New algorithm to model protein-protein recognition based on surface complementarity
Walls, P. H., & Sternberg, M. J. E. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90506-f · Cited by 151 · see citing works
Protein docking using a genetic algorithm
Gardiner, E. J., Willett, P., & Artymiuk, P. J. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1070 · Cited by 129 · see citing works
A Combinatorial Approach to Protein Docking with Flexible Side Chains
Althaus, E., Kohlbacher, O., Lenhof, H., & Müller, P. (2000) · Journal of Computational Biology · doi:10.1089/106652702760277336 · Cited by 81 · see citing works
Main-chain complementarity in protein-protein recognition
Vakser, I. A. (1996) · Protein Engineering Design and Selection · doi:10.1093/protein/9.9.741 · Cited by 46 · see citing works
Eisenstein, M., Shariv, I., Koren, G., et al. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0773 · Cited by 41 · see citing works
Construction of molecular assemblies via docking: Modeling of tetramers with D2 symmetry
Berchanski, A., & Eisenstein, M. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10480 · Cited by 41 · see citing works
Approaching the CAPRI challenge with an efficient geometry‐based docking
Inbar, Y., Schneidman‐Duhovny, D., Halperin, I., et al. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20561 · Cited by 24 · see citing works
Self-citationCrystal structure of tropomyosin at 7 �ngstroms resolution
Whitby, F. G., & Phillips, G. N., Jr. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(20000101)38:1
Flagged first, then by citations
Cited by
Sorted by citations
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
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888 · see citing works
Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577 · see citing works
Chen, Y.-C. (2015) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2014.12.001 · Cited by 611 · 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
Moitessier, N., Englebienne, P., Lee, D., Lawandi, J., & Corbeil, C. R. (2008) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707515 · Cited by 514 · 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
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes
Zaidman, D., Prilusky, J., & London, N. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00589 · Cited by 224 · see citing works
Computational approaches to therapeutic antibody design: established methods and emerging trends
Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbz095 · Cited by 219 · see citing works
“In fact, some docking methods such as ClusPro and PatchDock are able to automatically define the antibody CDRs in order to use this information during the docking process.”
MethodComputational prediction of protein–protein binding affinities
Siebenmorgen, T., & Zacharias, M. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1448 · Cited by 184 · see citing works
“Among the most common are geometric hashing methods to rapidly match geometric surface descriptors of proteins 38,39 and fast Fourier transform (FFT) correlation techniques 16,37,40,41 to efficiently locate overlaps between complementary protein surfaces.”
RosettaAntibody: antibody variable region homology modeling server
Sircar, A., Kim, E. T., & Gray, J. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp387 · Cited by 161 · see citing works
Principles for computational design of binding antibodies
Baran, D., Pszolla, M. G., Lapidoth, G. D., Norn, C., Dym, O., Unger, T., Albeck, S., Tyka, M. D., & Fleishman, S. J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707171114 · Cited by 136 · see citing works
Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
Eguchi, R. R., Choe, C. A., & Huang, P.-S. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010271 · Cited by 141 · see citing works
Lapidoth, G. D., Baran, D., Pszolla, G. M., Norn, C., Alon, A., Tyka, M. D., & Fleishman, S. J. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24779 · Cited by 107 · see citing works
Hot-spot analysis for drug discovery targeting protein-protein interactions
Rosell, M., & Fernández-Recio, J. (2018) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1430763 · Cited by 105 · see citing works
Gao, J., Mfuh, A., Amako, Y., & Woo, C. M. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.7b11639 · Cited by 102 · see citing works
Krawczyk, K., Baker, T., Shi, J., & Deane, C. M. (2013) · Protein Engineering Design and Selection · doi:10.1093/protein/gzt043 · Cited by 87 · see citing works
Chavez, J. D., Cilia, M., Weisbrod, C. R., Ju, H.-J., Eng, J. K., Gray, S. M., & Bruce, J. E. (2012) · Journal of Proteome Research · doi:10.1021/pr300041t · Cited by 69 · see citing works
Nithin, C., Ghosh, P., & Bujnicki, J. M. (2018) · Genes · doi:10.3390/genes9090432 · Cited by 48 · see citing works
Hernandez, C. C., Tian, X., Hu, N., Shen, W., Catron, M. A., Yang, Y., Chen, J., Jiang, Y., Zhang, Y., & Macdonald, R. L. (2021) · Brain Communications · doi:10.1093/braincomms/fcab033 · Cited by 43 · see citing works
Genetic interaction mapping informs integrative structure determination of protein complexes
Braberg, H., Echeverria, I., Bohn, S., Cimermancic, P., Shiver, A., Alexander, R., Xu, J., Shales, M., Dronamraju, R., Jiang, S., et al. (2020) · Science · doi:10.1126/science.aaz4910 · Cited by 37 · see citing works
Flexible backbone assembly and refinement of symmetrical homomeric complexes
Roy Burman, S. S., Yovanno, R. A., & Gray, J. J. (2019) · Structure · doi:10.1016/j.str.2019.03.014 · Cited by 18 · see citing works
Molecular characterization of human melanocortin-5 receptor ligand-receptor interaction
Yang, Y., Mishra, V. K., Chen, M., Duffee, E., Dimmitt, R., & Harmon, C. M. (2013) · Biochemistry · doi:10.1021/bi3013593 · Cited by 17 · see citing works
Refinement of protein-protein complexes in contact map space with metadynamics simulations
Pfeiffenberger, E., & Bates, P. A. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25612 · Cited by 15 · see citing works
- Authors
- Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J.
- Affiliations
- Tel Aviv University (IL)
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W363-W367
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1160241
- OpenAlex
- W2151460035
- Cited by
- 3,018
- References
- 29
- Citations by year
- 2026: 55 · 2025: 103 · 2024: 188 · 2023: 252 · 2022: 338 · 2021: 342 · 2020: 314 · 2019: 199 · 2018: 188 · 2017: 164 · 2016: 188 · 2015: 134 · 2014: 120 · 2013: 130 · 2012: 89
- FWCI
- 5.16
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Health and Human Services
- Israel Science Foundation
- Tel Aviv University
- National Institutes of Health (n01co12400-79-0-22, NO1-CO12400)
- National Cancer Institute (N01CO12400, N01-CO-012400, NO1‐CO‐12400)
- 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
- molecular docking, protein-protein docking, cyclic symmetry, web server, structure prediction
- MeSH terms
- Algorithms, Ligands, Protein Conformation, Software, User-Computer Interface, Internet, Multiprotein Complexes
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
