{"title":"第22.5章剑桥结构数据库在蛋白质晶体学中的相关性","authors":"F. Allen, J. Cole, M. Verdonk","doi":"10.1107/97809553602060000889","DOIUrl":null,"url":null,"abstract":"The importance of high-resolution crystal structure data of small molecules to protein crystallography is highlighted. Specific areas covered include: mean molecular dimensions for peptidic fragments and other biologically important substructures, conformational information, hydrogen-bond geometries and their directionality, and other strong non-covalent interactions. The value of the IsoStar knowledge base of intermolecular interactions, derived from the CSD and from protein–ligand complexes in the PDB, is illustrated. The value of structural information from small molecules to our understanding of protein–ligand binding is also discussed, together with examples of how this information is important in the prediction of ligand binding modes and in software tools for protein–ligand docking. \n \n \nKeywords: \n \nCambridge Structural Database; \ndatabases; \nhydrogen bonding; \nintermolecular interactions; \nIsoStar; \nmetal coordination geometry; \nnonbonded interactions; \nProtein Data Bank; \nprotein–ligand interactions; \nstructure validation; \nvan der Waals radii","PeriodicalId":338076,"journal":{"name":"International Tables for Crystallography","volume":"25 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2012-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Chapter 22.5 The relevance of the Cambridge Structural Database in protein crystallography\",\"authors\":\"F. Allen, J. Cole, M. Verdonk\",\"doi\":\"10.1107/97809553602060000889\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The importance of high-resolution crystal structure data of small molecules to protein crystallography is highlighted. Specific areas covered include: mean molecular dimensions for peptidic fragments and other biologically important substructures, conformational information, hydrogen-bond geometries and their directionality, and other strong non-covalent interactions. The value of the IsoStar knowledge base of intermolecular interactions, derived from the CSD and from protein–ligand complexes in the PDB, is illustrated. The value of structural information from small molecules to our understanding of protein–ligand binding is also discussed, together with examples of how this information is important in the prediction of ligand binding modes and in software tools for protein–ligand docking. \\n \\n \\nKeywords: \\n \\nCambridge Structural Database; \\ndatabases; \\nhydrogen bonding; \\nintermolecular interactions; \\nIsoStar; \\nmetal coordination geometry; \\nnonbonded interactions; \\nProtein Data Bank; \\nprotein–ligand interactions; \\nstructure validation; \\nvan der Waals radii\",\"PeriodicalId\":338076,\"journal\":{\"name\":\"International Tables for Crystallography\",\"volume\":\"25 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2012-04-14\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International Tables for Crystallography\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1107/97809553602060000889\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Tables for Crystallography","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1107/97809553602060000889","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Chapter 22.5 The relevance of the Cambridge Structural Database in protein crystallography
The importance of high-resolution crystal structure data of small molecules to protein crystallography is highlighted. Specific areas covered include: mean molecular dimensions for peptidic fragments and other biologically important substructures, conformational information, hydrogen-bond geometries and their directionality, and other strong non-covalent interactions. The value of the IsoStar knowledge base of intermolecular interactions, derived from the CSD and from protein–ligand complexes in the PDB, is illustrated. The value of structural information from small molecules to our understanding of protein–ligand binding is also discussed, together with examples of how this information is important in the prediction of ligand binding modes and in software tools for protein–ligand docking.
Keywords:
Cambridge Structural Database;
databases;
hydrogen bonding;
intermolecular interactions;
IsoStar;
metal coordination geometry;
nonbonded interactions;
Protein Data Bank;
protein–ligand interactions;
structure validation;
van der Waals radii