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SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations

文献类型：期刊论文

作者Sun, Zhaoxi3,4; He, Qiaole6; Li, Xiao1; Zhu, Zhengdan2,5
刊名JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
出版日期2020-05-01
卷号34期号:5页码:589-600
ISSN号0920-654X
关键词Free energy calculation Binding pose Binding affinity Spherical coordinates SAMPL6
DOI10.1007/s10822-020-00294-1
通讯作者Sun, Zhaoxi(proszx@163.com)
英文摘要Host-guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host-guest systems in the SAMPL6 challenge. By biasing the spherical coordinates describing the relative position of the host and the guest, the initial-configuration-induced bias vanishes and all possible binding poses are explored. The agreement between the predictions and the experimental results and the observation of new binding poses indicate that the volume-based technique serves as a nice candidate for the calculation of binding free energies and the search of the binding poses.
WOS关键词ENTROPY-ENTHALPY COMPENSATION ; SOLVATION FREE-ENERGIES ; MOLECULAR-DYNAMICS ; LIGAND-BINDING ; VARIANCE MINIMIZATION ; DRUG DISCOVERY ; FORCE-FIELDS ; SIDE-CHAIN ; WATER ; PREDICTION
WOS研究方向Biochemistry & Molecular Biology ; Biophysics ; Computer Science
语种英语
出版者SPRINGER
WOS记录号WOS:000524870100010
源URL[http://119.78.100.183/handle/2S10ELR8/281081]  
专题中国科学院上海药物研究所
通讯作者Sun, Zhaoxi
作者单位1.Univ Grenoble Alpes, Phys Engn Earth Environm Mech PhITEM, F-38000 Grenoble, France
2.Chinese Acad Sci, Drug Discovery & Design Ctr, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China
3.East China Normal Univ, Sch Chem & Mol Engn, State Key Lab Precis Spect, Shanghai 200062, Peoples R China
4.Forschungszentrum Julich, Computat Biomed IAS 5 INM 9, D-52425 Julich, Germany
5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
6.East China Univ Sci & Technol, Sch Biotechnol, Shanghai 200237, Peoples R China
推荐引用方式
GB/T 7714		 Sun, Zhaoxi,He, Qiaole,Li, Xiao,et al. SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations[J]. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,2020,34(5):589-600.
APA Sun, Zhaoxi,He, Qiaole,Li, Xiao,&Zhu, Zhengdan.(2020).SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,34(5),589-600.
MLA Sun, Zhaoxi,et al."SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations".JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 34.5(2020):589-600.

入库方式： OAI收割

来源：上海药物研究所

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