Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation
文献类型：期刊论文
| 作者 | Pei, JF; Wang, Q; Zhou, JJ; Lai, LH |
| 刊名 | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
 |
| 出版日期 | 2004-12-01 |
| 卷号 | 57期号:4页码:651-664 |
| 关键词 | ASP log P solvent-accessible surface area ASPLOGOP protein-ligand complex conformation-dependent SCORE |
| ISSN号 | 0887-3585 |
| 其他题名 | Proteins |
| 中文摘要 | 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. |
| 英文摘要 | 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 关键词[WOS] | ACCESSIBLE SURFACE-AREAS ; EMPIRICAL SCORING FUNCTIONS ; MOLECULAR-DYNAMICS ; ADDITIVE METHOD ; PREDICTION ; AFFINITY ; MODEL ; VALIDATION ; PEPTIDES ; COMPLEX |
| 收录类别 | SCI |
| 原文出处 | |
| 语种 | 英语 |
| WOS记录号 | WOS:000225351100002 |
| 公开日期 | 2013-11-05 |
| 版本 | 出版稿 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/4929]  |
| 专题 | 过程工程研究所_研究所（批量导入） |
| 作者单位 | 1.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 |
| 推荐引用方式 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. |
入库方式： OAI收割
来源：过程工程研究所
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