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	A statistical approach to the prediction of pk(a) values in proteins
	He, Yun; Xu, Jialin; Pan, Xian-Ming
刊名	Proteins-structure function and bioinformatics
	2007-10-01
卷号	69期号:1页码:75-82
关键词	Protein ionizable Residues pka prediction Residue interaction Protonation Deprotonation Electrostatic Interaction
ISSN号	0887-3585
DOI	10.1002/prot.21478
通讯作者	Pan, xian-ming(pan-xm@mail.tsinghua.edu.cn)
英文摘要	We propose a simple model for the calculation of pk. values of ionizable residues in proteins. it is based on the premise that the pk, shift of ionizable residues is linearly correlated to the interaction between a particular residue and the local environment created by the surrounding residues. despite its simplicity, the model displays good prediction performance. under the sixfold cross test prediction over a data set of 405 experimental pka values in 73 protein chains with known structures, the root-mean-square deviation (rmsd) between the experimental and calculated pka was found to be 0.77. the accuracy of this model increases with increasing size of the data set: the rmsd is 0.609, for glutamate (the largest data set with 141 sites) and similar to 1 ph unit for lysine, with a data set containing 45 sites.
WOS关键词	OVOMUCOID 3RD DOMAIN ; CARBOXYL GROUPS ; ELECTROSTATIC INTERACTIONS ; IONIZATION EQUILIBRIA ; DIELECTRIC-CONSTANTS ; FREE-ENERGY ; CHARGE INTERACTIONS ; IONIZABLE RESIDUES ; SOLVATED PROTEINS ; TITRATABLE GROUPS
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemistry & Molecular Biology ; Biophysics
语种	英语
出版者	WILEY-LISS
WOS记录号	WOS:000249189000008
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2380173
专题	中国科学院大学
通讯作者	Pan, Xian-Ming
作者单位	1.Tsing Hua Univ, Dept Biol Sci & Biotechnol, Beijing 100084, Peoples R China 2.Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China 3.Grad Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	He, Yun,Xu, Jialin,Pan, Xian-Ming. A statistical approach to the prediction of pk(a) values in proteins[J]. Proteins-structure function and bioinformatics,2007,69(1):75-82.
APA	He, Yun,Xu, Jialin,&Pan, Xian-Ming.(2007).A statistical approach to the prediction of pk(a) values in proteins.Proteins-structure function and bioinformatics,69(1),75-82.
MLA	He, Yun,et al."A statistical approach to the prediction of pk(a) values in proteins".Proteins-structure function and bioinformatics 69.1(2007):75-82.

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