GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states

doi:10.1186/s12859-024-05962-9

	GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states
	Liu, Fan 1,2; Zhou, Han 1,2,3; Li, Xiaonong 3; Zhou, Liangliang 3; Yu, Chungong 1,4; Zhang, Haicang 1,4; Bu, Dongbo 1,4,5; Liang, Xinmiao 1,2,3
	2024-11-04
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	25 期号:1 页码:16
摘要	G-protein coupled receptors (GPCRs), the largest family of membrane proteins in human body, involve a great variety of biological processes and thus have become highly valuable drug targets. By binding with ligands (e.g., drugs), GPCRs switch between active and inactive conformational states, thereby performing functions such as signal transmission. The changes in binding pockets under different states are important for a better understanding of drug-target interactions. Therefore it is critical, as well as a practical need, to obtain binding sites in human GPCR structures. We report a database (called GPCR-BSD) that collects 127,990 predicted binding sites of 803 GPCRs under active and inactive states (thus 1,606 structures in total). The binding sites were identified from the predicted GPCR structures by executing three geometric-based pocket prediction methods, fpocket, CavityPlus and GHECOM. The server provides query, visualization, and comparison of the predicted binding sites for both GPCR predicted and experimentally determined structures recorded in PDB. We evaluated the identified pockets of 132 experimentally determined human GPCR structures in terms of pocket residue coverage, pocket center distance and redocking accuracy. The evaluation showed that fpocket and CavityPlus methods performed better and successfully predicted orthosteric binding sites in over 60% of the 132 experimentally determined structures. The GPCR Binding Site database is freely accessible at https://gpcrbs.bigdata.jcmsc.cn. This study not only provides a systematic evaluation of the commonly-used fpocket and CavityPlus methods for the first time but also meets the need for binding site information in GPCR studies.
关键词	G-protein coupled receptor State-specific structure Binding site Key residue Database
DOI	10.1186/s12859-024-05962-9
收录类别	SCI
语种	英语
资助项目	Innovation Program of Science and Research of DICP, CAS
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:001348653100001
出版者	BMC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/39474
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu, Dongbo; Liang, Xinmiao
作者单位	1.Univ Chinese Acad Sci, Beijing 101408, Peoples R China 2.Chinese Acad Sci, Dalian Inst Chem Phys, Key Lab Phytochemistry & Nat Med, Dalian 116023, Liaoning, Peoples R China 3.Ganjiang Chinese Med Innovat Ctr, Jiangxi Prov Key Lab Pharmacodynam Mat Basis Tradi, Nanchang 330000, Jiangxi, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, SKLP, Beijing, Peoples R China 5.Cent China Inst Artificial Intelligence, Zhengzhou 450046, Henan, Peoples R China
推荐引用方式 GB/T 7714	Liu, Fan,Zhou, Han,Li, Xiaonong,et al. GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states[J]. BMC BIOINFORMATICS,2024,25(1):16.
APA	Liu, Fan.,Zhou, Han.,Li, Xiaonong.,Zhou, Liangliang.,Yu, Chungong.,...&Liang, Xinmiao.(2024).GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states.BMC BIOINFORMATICS,25(1),16.
MLA	Liu, Fan,et al."GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states".BMC BIOINFORMATICS 25.1(2024):16.