期刊
JOURNAL OF CHEMICAL INFORMATION AND MODELING
卷 50, 期 8, 页码 1378-1386出版社
AMER CHEMICAL SOC
DOI: 10.1021/ci100182c
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资金
- National Science and Technology Major Project [2009ZX09501-010]
- State Key Program of Basic Research of China [009CB918502]
- Science and Technology Commission of Shanghai Municipality [08DZ1980200]
Protein kinases are attractive targets for therapeutic interventions in many diseases. Due to their importance in drug discovery, a kinase family-specific potential of mean force (PMF) scoring function, kinase-PMF, was developed to assess the binding of ATP-competitive kinase inhibitors. It is hypothesized that target-specific PMF scoring functions may achieve increased performance in scoring along with the growth of the PDB database. The kinase-PMF inherits the functions and atom types in PMF04 and uses a kinase data set of 872 complexes to derive the potentials. The performance of kinase-PMF was evaluated with an external test set containing 128 kinase crystal structures. We compared it with eight scoring functions commonly used in computer-aided drug design, either in terms of the retrieval rate of retrieving right conformations or a virtual screening study. The evaluation results clearly demonstrate that a target-specific scoring function is a promising way to improve prediction power in structure-based drug design compared with other general scoring functions. To provide this rescoring service for researchers, a publicly accessible Web site was established at http://202.127.30.184:8080/scoring/index.jsp.
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