The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
ZRANK: Reranking protein docking predictions with an optimized energy function
Abstract
Protein–protein docking requires fast and effective methods to quickly discriminate correct from incorrect predictions generated by initial‐stage docking. We have developed and tested a scoring function that utilizes detailed electrostatics, van der Waals, and desolvation to rescore initial‐stage docking predictions. Weights for the scoring terms were optimized for a set of test cases, and this optimized function was then tested on an independent set of nonredundant cases. This program, named ZRANK, is shown to significantly improve the success rate over the initial ZDOCK rankings across a large benchmark. The amount of test cases with No. 1 ranked hits increased from 2 to 11 and from 6 to 12 when predictions from two ZDOCK versions were considered. ZRANK can be applied either as a refinement protocol in itself or as a preprocessing stage to enrich the well‐ranked hits prior to further refinement. Proteins 2007. © 2007 Wiley‐Liss, Inc.
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Cited by
Ihle, N. T., Byers, L. A., Kim, E. S., Saintigny, P., Lee, J. J., Blumenschein, G. R., Tsao, A., Liu, S., Larsen, J. E., Wang, J., et al. (2012) · JNCI: Journal of the National Cancer Institute · doi:10.1093/jnci/djr523 · Cited by 532
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
Self-citationBenchmarking 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
Self-citationCPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
de Vries, S. J., & Bonvin, A. M. J. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017695 · Cited by 324
Metadata
- Authors
- Pierce, B., & Weng, Z.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2007-05
- Volume
- 67
- Issue
- 4
- Pages
- 1078-1086
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2129454543
- Cited by
- 444
- References
- 31
- FWCI
- 5.75
- Type
- journal article
- Language
- en
- Open access
- closed
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