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

doi:10.1007/s10822-020-00294-1

	SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations
	Sun, Zhaoxi 1,2; He, Qiaole 3; Li, Xiao 4; Zhu, Zhengdan 5,6
刊名	JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
	2020-05-01
卷号	34 期号:5 页码:589-600
关键词	Free energy calculation Binding pose Binding affinity Spherical coordinates SAMPL6
ISSN号	0920-654X
DOI	10.1007/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
内容类型	期刊论文
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.Forschungszentrum Julich, Computat Biomed IAS 5 INM 9, D-52425 Julich, Germany 2.East China Normal Univ, Sch Chem & Mol Engn, State Key Lab Precis Spect, Shanghai 200062, Peoples R China 3.East China Univ Sci & Technol, Sch Biotechnol, Shanghai 200237, Peoples R China 4.Univ Grenoble Alpes, Phys Engn Earth Environm Mech PhITEM, F-38000 Grenoble, France 5.Chinese Acad Sci, Drug Discovery & Design Ctr, Shanghai Inst Mat Med, CAS Key Lab Receptor Res, Shanghai 201203, Peoples R China 6.Univ Chinese Acad Sci, Beijing 100049, 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.