The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
Open accessAbstract
Motivation: Predicting protein interactions is one of the most challenging problems in functional genomics. Given two proteins known to interact, current docking methods evaluate billions of docked conformations by simple scoring functions, and in addition to near-native structures yield many false positives, i.e. structures with good surface complementarity but far from the native. Results: We have developed a fast algorithm for filtering docked conformations with good surface complementarity, and ranking them based on their clustering properties. The free energy filters select complexes with lowest desolvation and electrostatic energies. Clustering is then used to smooth the local minima and to select the ones with the broadest energy wells—a property associated with the free energy at the binding site. The robustness of the method was tested on sets of 2000 docked conformations generated for 48 pairs of interacting proteins. In 31 of these cases, the top 10 predictions include at least one near-native complex, with an average RMSD of 5 Å from the native structure. The docking and discrimination method also provides good results for a number of complexes that were used as targets in the Critical Assessment of PRedictions of Interactions experiment. Availability: The fully automated docking and discrimination server ClusPro can be found at http://structure.bu.edu
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
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ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393 · cited 3×
“We have tested the discrimination step of the method on the sets of 2000 docked conformations, developed by Chen and Weng (2003) for 48 protein pairs.”
BackgroundMethodInfluentialPrinciples of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
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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
Self-citationDissecting protein–protein recognition sites
Chakrabarti, P., & Janin, J. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10085 · Cited by 570
Protein docking using spherical polar Fourier correlations
Ritchie, D. W., & Kemp, G. J. L. (2000) · Proteins: Structure, Function, and Genetics · doi:10.1002/(sici)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6 · Cited by 563
Determination of atomic desolvation energies from the structures of crystallized proteins
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PIPER: An FFT‐based protein docking program with pairwise potentials
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Sievers, Q. L., Petzold, G., Bunker, R. D., Renneville, A., Słabicki, M., Liddicoat, B. J., Abdulrahman, W., Mikkelsen, T., Ebert, B. L., & Thomä, N. H. (2018) · Science · doi:10.1126/science.aat0572 · Cited by 537
Predicting Protein–Protein Interactions from the Molecular to the Proteome Level
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Greenbaum, J. A., Andersen, P. H., Blythe, M., Bui, H., Cachau, R. E., Crowe, J., Davies, M., Kolaskar, A. S., Lund, O., Morrison, S., et al. (2007) · Journal of Molecular Recognition · doi:10.1002/jmr.815 · Cited by 244
Metadata
- Authors
- Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-01
- Volume
- 20
- Issue
- 1
- Pages
- 45-50
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112743424
- Cited by
- 855
- References
- 27
- FWCI
- 4.93
- Type
- journal article
- Language
- en
- Open access
- bronze
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