期刊
NUCLEIC ACIDS RESEARCH
卷 38, 期 -, 页码 W417-W423出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkq396
关键词
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资金
- TUBITAK-BIDEB [2218]
- Betil Fund [EU FP6-2004-ACC-SSA-2, 517991]
- Turkish Academy of Sciences (TUBA)
- State Planning Organization of the Turkish Republic [DPT 2010K120670]
DNABINDPROT is designed to predict DNA-binding residues, based on the fluctuations of residues in high-frequency modes by the Gaussian network model. The residue pairs that display high mean-square distance fluctuations are analyzed with respect to DNA binding, which are then filtered with their evolutionary conservation profiles and ranked according to their DNA-binding propensities. If the analyses are based on the exact outcome of fluctuations in the highest mode, using a conservation threshold of 5, the results have a sensitivity, specificity, precision and accuracy of 9.3%, 90.5%, 18.1% and 78.6%, respectively, on a dataset of 36 unbound-bound protein structure pairs. These values increase up to 24.3%, 93.4%, 45.3% and 83.3% for the respective cases, when the neighboring two residues are considered. The relatively low sensitivity appears with the identified residues being selective and susceptible more for the binding core residues rather than all DNA-binding residues. The predicted residues that are not tagged as DNA-binding residues are those whose fluctuations are coupled with DNA-binding sites. They are in close proximity as well as plausible for other functional residues, such as ligand and protein-protein interaction sites. DNABINDPROT is free and open to all users without login requirement available at: http://www.prc.boun.edu.tr/appserv/prc/dnabindprot/.
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