系统收集PDB数据库中的亲合性数据:PDBbind数据库的最新进展
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- 英文论文题名：PDB-wide collection of binding data:current status of the PDBbind database
- 论文作者：刘志海 ; 李嫣 ; 韩莉 ; 刘杰 ; 赵志雄 ; 聂伟 ; 刘宇晨 ; 王任小 ; Jie Li
- 英文论文作者：Zhihai Liu ; Yan Li ; Li Han ; Jie Li ; Jie Liu ; Zhixiong Zhao ; Wei Nie ; Yuchen Liu ; Renxiao Wang ; State Key Laboratory of Bioorganic and Natural Products Chemistry ; Shanghai Institute of Organic Chemistry ; Chinese Academy of Sciences
- 年：2016
- 作者机构：中国科学院上海有机化学研究所生命有机化学国家重点实验室;
- 论文关键词：PDBbind ; 亲合性 ; PDB数据库 ; 复合物
- 会议召开时间：2016-07-01
- 会议录名称：中国化学会第30届学术年会摘要集-第二十五分会：化学信息学与化学计量学
- 语种：中文
- 分类号：TP311.13;O641.3
- 学会代码：ZGHY
- 会议名称：中国化学会第30届学术年会-第二十五分会 ; 化学信息学与化学计量学
- 会议地点：中国辽宁大连
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：1
- 文件大小：169k
- 原文格式：D
- 会议级别：全国
摘要
生物大分子与有机小分子配体之间的相互识别在各种生命活动过程中扮演很重要的角色。生物大分子复合物的三维结构和亲合性信息是描述这些生命过程的底层机理所不可或缺的信息。PDBbind数据库的创建目的是完整收录Protein Data Bank(PDB)数据库中通过实验测定的亲合性数据。由此为生物大分子复合物的结构信息和能量信息提供相互联系,而这些信息在计算模拟研究中非常重要。自2004年首次公开发布以来,PDBbind数据库保持每年更新一次。即将发布的最新2016版中将大约包含16000个复合物的亲合性和三维结构信息。我们的研究表明,PDBbind中的数据信息与其他的同类大型数据库,比如ChEMBL具有很大的互补性,具有独特的研究价值。PDBbind中所有的数据都可以通过如下网站免费获取和使用:http://www.pdbbind-cn.org http://www.pdbbind.org.cn
Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes.Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event.The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank(PDB).It thus provides the linkage between structural information and energetic properties of biomolecular complexes,which is especially desirable for computational studies or statistical analyses.Since its first public release in 2004,the PDBbind database has been updated on an annual basis.The latest v2016 to be released will provide experimental binding affinity data for about 16000 biomolecular complexes in PDB.
Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes.Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event.The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank(PDB).It thus provides the linkage between structural information and energetic properties of biomolecular complexes,which is especially desirable for computational studies or statistical analyses.Since its first public release in 2004,the PDBbind database has been updated on an annual basis.The latest v2016 to be released will provide experimental binding affinity data for about 16000 biomolecular complexes in PDB.
引文
[1]Liu Z.H.;Li Y.;Han L.;Li J.;Liu J.;Zhao Z.X.;Nie W.,Liu Y.C.,Wang R.X.,Bioinformatics,2015,31:405.
[2]Liu Z.H.;Li J.;Liu J.;Liu Y.C.;Nie W.;Han L.;Wang R.X.,Mol.Informatics,2015,34:568.
[3]Li Y.;Han L.;Liu Z.H.;Wang R.X.,J.Chem.Inf.Model,2014,54:1717.
[4]Li Y.;Liu Z.H.;Li J.;Han L.;Liu J.;Zhao Z.X.;Wang R.X.,J.Chem.Inf.Model,2014,54:1700.
[5]Wang,R.;Fang,X.;Lu,Y.;Yang,C.-Y.;Wang,S.,J.Med.Chem.,2005,48:4111.
[6]Wang,R.;Fang,X.;Lu,Y;Wang,S.,J.Med.Chem.,2004,47:2977.
[2]Liu Z.H.;Li J.;Liu J.;Liu Y.C.;Nie W.;Han L.;Wang R.X.,Mol.Informatics,2015,34:568.
[3]Li Y.;Han L.;Liu Z.H.;Wang R.X.,J.Chem.Inf.Model,2014,54:1717.
[4]Li Y.;Liu Z.H.;Li J.;Han L.;Liu J.;Zhao Z.X.;Wang R.X.,J.Chem.Inf.Model,2014,54:1700.
[5]Wang,R.;Fang,X.;Lu,Y.;Yang,C.-Y.;Wang,S.,J.Med.Chem.,2005,48:4111.
[6]Wang,R.;Fang,X.;Lu,Y;Wang,S.,J.Med.Chem.,2004,47:2977.