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Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors. Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes. Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches.", "publicationTitle": "Nature Reviews. 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"language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-06-23T14:00:44Z", "dateModified": "2014-06-23T14:00:44Z" } }, { "key": "JQA82STQ", "version": 51, "library": { "type": "group", "id": 63343, "name": "Hynšt Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/hynt_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/63343/items/JQA82STQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/hynt_jakub/items/JQA82STQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 828248, "username": "Hynšt Jakub", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hynt_jakub", "type": "text/html" } } }, "creatorSummary": "Gilboa-Garber", "parsedDate": "1982", "numChildren": 0 }, "data": { "key": "JQA82STQ", "version": 51, "itemType": "bookSection", "title": "[32] Pseudomonas aeruginosa lectins", "creators": [ { "creatorType": "author", "firstName": "Nechama", "lastName": "Gilboa-Garber" } ], "abstractNote": "", "bookTitle": "Methods in Enzymology", "series": "", "seriesNumber": "", "volume": "83", "numberOfVolumes": "", "edition": "", "date": "1982", "publisher": "Elsevier", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "378-385", "ISBN": "9780121819835", "DOI": "", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/0076687982830346", "accessDate": "2014-06-23T13:50:13Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "BWFSI4QN" ], "relations": {}, "dateAdded": "2014-06-23T13:50:13Z", "dateModified": "2014-06-23T13:50:13Z" } }, { "key": "2UTSCZSZ", "version": 50, "library": { "type": "group", "id": 63343, "name": "Hynšt Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/hynt_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/63343/items/2UTSCZSZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/hynt_jakub/items/2UTSCZSZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 828248, "username": "Hynšt Jakub", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hynt_jakub", "type": "text/html" } } }, "creatorSummary": "Mitchell et al.", "parsedDate": "2005-02-15", "numChildren": 1 }, "data": { "key": "2UTSCZSZ", "version": 50, "itemType": "journalArticle", "title": "High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL: 1.0 A resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches", "creators": [ { "creatorType": "author", "firstName": "Edward P.", "lastName": "Mitchell" }, { "creatorType": "author", "firstName": "Charles", "lastName": "Sabin" }, { "creatorType": "author", "firstName": "Lenka", "lastName": "Snajdrová" }, { "creatorType": "author", "firstName": "Martina", "lastName": "Pokorná" }, { "creatorType": "author", "firstName": "Stéphanie", "lastName": "Perret" }, { "creatorType": "author", "firstName": "Catherine", "lastName": "Gautier" }, { "creatorType": "author", "firstName": "Ctirad", "lastName": "Hofr" }, { "creatorType": "author", "firstName": "Nechama", "lastName": "Gilboa-Garber" }, { "creatorType": "author", "firstName": "Jaroslav", "lastName": "Koca" }, { "creatorType": "author", "firstName": "Michaela", "lastName": "Wimmerová" }, { "creatorType": "author", "firstName": "Anne", "lastName": "Imberty" } ], "abstractNote": "PA-IIL is a fucose-binding lectin from Pseudomonas aeruginosa that is closely related to the virulence factors of the bacterium. Previous structural studies have revealed a new carbohydrate-binding mode with direct involvement of two calcium ions (Mitchell E, Houles C, Sudakevitz D, Wimmerova M, Gautier C, Perez S, Wu AM, Gilboa-Garber N, Imberty A. Structural basis for selective recognition of oligosaccharides from cystic fibrosis patients by the lectin PA-IIL of Pseudomonas aeruginosa. Nat Struct Biol 2002;9:918-921). A combination of thermodynamic, structural, and computational methods has been used to study the basis of the high affinity for the monosaccharide ligand. A titration microcalorimetry study indicated that the high affinity is enthalpy driven. The crystal structure of the tetrameric PA-IIL in complex with fucose and calcium was refined to 1.0 A resolution and, in combination with modeling, allowed a proposal to be made for the hydrogen-bond network in the binding site. Calculations of partial charges using ab initio computational chemistry methods indicated that extensive delocalization of charges between the calcium ions, the side chains of the protein-binding site and the carbohydrate ligand is responsible for the high enthalpy of binding and therefore for the unusually high affinity observed for this unique mode of carbohydrate recognition.", "publicationTitle": "Proteins", "publisher": "", "place": "", "date": "Feb 15, 2005", "volume": "58", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "735-746", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proteins", "DOI": "10.1002/prot.20330", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1097-0134", "archive": "", "archiveLocation": "", "shortTitle": "High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 15573375", "tags": [ { "tag": "Adhesins, Bacterial", "type": 1 }, { "tag": "Amino Acid Sequence", "type": 1 }, { "tag": "Bacterial Proteins", "type": 1 }, { "tag": "Binding Sites", "type": 1 }, { "tag": "Calcium", "type": 1 }, { "tag": "Calorimetry", "type": 1 }, { "tag": "Carbohydrates", "type": 1 }, { "tag": "Computational Biology", "type": 1 }, { "tag": "Crystallography, X-Ray", "type": 1 }, { "tag": "Cystic Fibrosis", "type": 1 }, { "tag": "Escherichia coli", "type": 1 }, { "tag": "Fucose", "type": 1 }, { "tag": "Hemagglutinins", "type": 1 }, { "tag": "Hot Temperature", "type": 1 }, { "tag": "Hydrogen Bonding", "type": 1 }, { "tag": "Hydrogen-Ion Concentration", "type": 1 }, { "tag": "Ions", "type": 1 }, { "tag": "Lectins", "type": 1 }, { "tag": "Ligands", "type": 1 }, { "tag": "Models, Molecular", "type": 1 }, { "tag": "Molecular Conformation", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Plasmids", "type": 1 }, { "tag": "Protein Binding", "type": 1 }, { "tag": "Proteins", "type": 1 }, { "tag": "Protons", "type": 1 }, { "tag": "Pseudomonas aeruginosa", "type": 1 }, { "tag": "Recombinant Proteins", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Temperature", "type": 1 }, { "tag": "Thermodynamics", "type": 1 } ], "collections": [ "BWFSI4QN" ], "relations": {}, "dateAdded": "2014-06-23T13:44:09Z", "dateModified": "2014-06-23T13:44:09Z" } } ]