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Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation
Alternative TitleProteins
Pei, JF; Wang, Q; Zhou, JJ; Lai, LH
2004-12-01
Source PublicationPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
ISSN0887-3585
Volume57Issue:4Pages:651-664
AbstractSolvation energy calculation is one of the main difficulties for the estimation of protein-ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein-ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of proteinligand binding free energy predictions. The ASP set, designed to handle both proteins and organic compounds and derived from experimental n-octanol/ water partition coefficient (log P) data, contains 100 atom types (united model that treats hydrogen atoms implicitly) or 119 atom types (all-atom model that treats hydrogen atoms explicitly). By using this unified ASP set, an algorithm was developed for solvation energy calculation and was further integrated into a score function for predicting protein-ligand binding affinity. The score function reproduced the absolute binding free energies of a test set of 50 protein-ligand complexes with a standard error of 8.31 kJ/mol. As a byproduct, a conformation-dependent log P calculation algorithm named ASPLOGP was also implemented. The predictive results of ASPLOGP for a test set of 138 compounds were r = 0.968, s = 0.344 for the all-atom model and r = 0.962, s = 0.367 for the united model, which were better than previous conformation-dependent approaches and comparable to fragmental and atom-based methods. ASPLOGP also gave good predictive results for small peptides. The score function based on the ASP model can be applied widely in protein-ligand interaction studies and structure-based drug design. (C) 2004 Wiley-Liss, Inc.; Solvation energy calculation is one of the main difficulties for the estimation of protein-ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein-ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of proteinligand binding free energy predictions. The ASP set, designed to handle both proteins and organic compounds and derived from experimental n-octanol/ water partition coefficient (log P) data, contains 100 atom types (united model that treats hydrogen atoms implicitly) or 119 atom types (all-atom model that treats hydrogen atoms explicitly). By using this unified ASP set, an algorithm was developed for solvation energy calculation and was further integrated into a score function for predicting protein-ligand binding affinity. The score function reproduced the absolute binding free energies of a test set of 50 protein-ligand complexes with a standard error of 8.31 kJ/mol. As a byproduct, a conformation-dependent log P calculation algorithm named ASPLOGP was also implemented. The predictive results of ASPLOGP for a test set of 138 compounds were r = 0.968, s = 0.344 for the all-atom model and r = 0.962, s = 0.367 for the united model, which were better than previous conformation-dependent approaches and comparable to fragmental and atom-based methods. ASPLOGP also gave good predictive results for small peptides. The score function based on the ASP model can be applied widely in protein-ligand interaction studies and structure-based drug design. (C) 2004 Wiley-Liss, Inc.
KeywordAsp Log p Solvent-accessible Surface Area Asplogop Protein-ligand Complex Conformation-dependent Score
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
DOI10.1002/prot.20198
URL查看原文
Indexed BySCI
Language英语
WOS KeywordACCESSIBLE SURFACE-AREAS ; EMPIRICAL SCORING FUNCTIONS ; MOLECULAR-DYNAMICS ; ADDITIVE METHOD ; PREDICTION ; AFFINITY ; MODEL ; VALIDATION ; PEPTIDES ; COMPLEX
WOS Research AreaBiochemistry & Molecular Biology ; Biophysics
WOS SubjectBiochemistry & Molecular Biology ; Biophysics
WOS IDWOS:000225351100002
Citation statistics
Cited Times:60[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.ipe.ac.cn/handle/122111/4929
Collection研究所(批量导入)
Affiliation1.Peking Univ, Coll Chem & Mol Engn, State Key Lab Struct Chem Stable & Unstable Speci, Beijing 100871, Peoples R China
2.Peking Univ, Ctr Theoret Biol, Beijing 100871, Peoples R China
3.Chinese Acad Sci, Inst Proc Engn, Beijing, Peoples R China
Recommended Citation
GB/T 7714
Pei, JF,Wang, Q,Zhou, JJ,et al. Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2004,57(4):651-664.
APA Pei, JF,Wang, Q,Zhou, JJ,&Lai, LH.(2004).Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,57(4),651-664.
MLA Pei, JF,et al."Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 57.4(2004):651-664.
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