The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Protein–protein docking benchmark 2.0: An update
Abstract
We present a new version of the Protein–Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound–unbound cases, with 52 rigid‐body cases, 13 medium‐difficulty cases, and 7 high‐difficulty cases with substantial conformational change. In addition, we retained 12 antibody–antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2 . Proteins 2005;60:214–216. © 2005 Wiley‐Liss, Inc.
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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
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
Self-citationAssessment of blind predictions of protein–protein interactions: Current status of docking methods
Méndez, R., Leplae, R., De Maria, L., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10393 · Cited by 418
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 344
Self-citationAtomic contact vectors in protein‐protein recognition
Mintseris, J., & Weng, Z. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10432 · Cited by 127
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Cited by
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 3,310
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
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 444
Self-citationVreven, 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
Self-citationMolecular docking as a popular tool in drug design, an in silico travel
de Ruyck, J., Brysbaert, G., Blossey, R., & Lensink, M. (2016) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s105289 · Cited by 346
Metadata
- Authors
- Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J., & Weng, Z.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2005-06-24
- Volume
- 60
- Issue
- 2
- Pages
- 214-216
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2014744153
- Cited by
- 278
- References
- 7
- FWCI
- 9.33
- Type
- journal article
- Language
- en
- Open access
- closed
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