Journal
BRIEFINGS IN BIOINFORMATICS
Volume 16, Issue 6, Pages 1025-1034Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbv009
Keywords
protein-protein interactions; protein interface prediction; interfacial residues; protein-protein complexes; protein models; web servers
Funding
- Louisiana Board of Regents through Board of Regents Support Fund [LEQSF(2012-15)-RD-A-05]
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It has been more than a decade since the completion of the Human Genome Project that provided us with a complete list of human proteins. The next obvious task is to figure out how various parts interact with each other. On that account, we review 10 methods for protein interface prediction, which are freely available as web servers. In addition, we comparatively evaluate their performance on a common data set comprising different quality target structures. We find that using experimental structures and high-quality homology models, structure-based methods outperform those using only protein sequences, with global template-based approaches providing the best performance. For moderate-quality models, sequence-based methods often perform better than those structure-based techniques that rely on fine atomic details. We note that post-processing protocols implemented in several methods quantitatively improve the results only for experimental structures, suggesting that these procedures should be tuned up for computer-generated models. Finally, we anticipate that advanced meta-prediction protocols are likely to enhance interface residue prediction. Notwithstanding further improvements, easily accessible web servers already provide the scientific community with convenient resources for the identification of protein-protein interaction sites.
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