Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 50, Issue 10, Pages 1906-1913Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ci100265x
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Funding
- Ministry of Higher Education, Science, and Technology of Slovenia [P1-0002]
- Slovenian Research Agency
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Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60 000 proteins or over 300 000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.
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