New Born radii deriving method for generalized Born model

doi:10.1021/ci0497408

CORC > 北京大学 > 化学与分子工程学院

	New Born radii deriving method for generalized Born model
	Zhang, W ; Hou, TJ ; Xu, XJ
刊名	journal of chemical information and modeling
	2005
关键词	HYDRATION SHELL-MODEL FREE-ENERGIES SOLUTE MOLECULES FORCE-FIELD SOLVATION PARAMETERS DYNAMICS WATER CONSISTENT SIMULATION
DOI	10.1021/ci0497408
英文摘要	Here we report a method to calculate Born radii, an important parameter used in a Generalized Born model. Traditional methods to derive Born radii are mostly based on a complicated formula, while our method is easier and more direct. Atoms are classified according to their atom type, and the Born radii of each type are obtained by fitting to experimental solvation free energy. The SMARTS language is used for the exact definition of atoms types, and Ullmann's subgraph isomorphism algorithm is used to deduce the environment. A generic algorithm is used for the parameter fitting because of its efficiency in searching a huge phase space, and its results are then optimized by using the conjugate gradient method. The final parameter set is fitting from a training set containing 357 molecules and is tested using a test set of 44 small organic molecules, and the average error is 0.58 kcal/mol for 36 neutral molecules and is 1.67 kcal/mol for 8 ions. The model is further tested under organic molecules, biopolymers, and a protein-inhibitor complex and yields reliable results in all these cases. This method can be used to accelerate molecular docking calculations.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000227982800011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Chemistry, Medicinal; Chemistry, Multidisciplinary; Computer Science, Information Systems; Computer Science, Interdisciplinary Applications; SCI(E); EI; PubMed; 4; ARTICLE; 1; 88-93; 45
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/199505]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Zhang, W,Hou, TJ,Xu, XJ. New Born radii deriving method for generalized Born model[J]. journal of chemical information and modeling,2005.
APA	Zhang, W,Hou, TJ,&Xu, XJ.(2005).New Born radii deriving method for generalized Born model.journal of chemical information and modeling.
MLA	Zhang, W,et al."New Born radii deriving method for generalized Born model".journal of chemical information and modeling (2005).