{ "labelLang" : "hun", "responseDate" : "2024-03-29 15:13", "content" : { "otype" : "JournalArticle", "mtid" : 2869502, "status" : "VALIDATED", "published" : true, "comment" : "Export Date: 27 January 2024; CODEN: BOINF", "unhandledTickets" : 0, "oldTimestamp" : "2018-08-10T09:54:14.000+0000", "deleted" : false, "oldId" : 2869502, "lastRefresh" : "2024-02-17T21:26:35.889+0000", "lastModified" : "2020-12-22T17:04:23.030+0000", "created" : "2015-03-22T21:54:04.000+0000", "creator" : { "otype" : "Author", "mtid" : 10001657, "link" : "/api/author/10001657", "label" : "Hetényi Csaba (Farmakoinformatika, molekulaszerkezet)", "familyName" : "Hetényi", "givenName" : "Csaba", "published" : true, "oldId" : 10001657, "snippet" : true }, "lastDuplumSearch" : "2024-01-27T17:44:54.035+0000", "adminApproved" : "2019-03-05T13:08:22.889+0000", "adminApprover" : { "otype" : "Admin", "mtid" : 10039043, "link" : "/api/admin/10039043", "label" : "Milánkovics Róbert (PTE ÁOK admin 4)", "familyName" : "Milánkovics", "givenName" : "Róbert", "published" : true, "oldId" : 10039043, "snippet" : true }, "validated" : "2019-07-08T12:55:45.204+0000", "validator" : { "otype" : "Admin", "mtid" : 10022707, "link" : "/api/admin/10022707", "label" : "Najbauerné Bacsics Zsuzsanna (PTE ÁOK admin 5_inaktív)", "familyName" : "Najbauerné Bacsics", "givenName" : "Zsuzsanna", "published" : true, "oldId" : 10022707, "snippet" : true }, "core" : true, "citation" : false, "publicationPending" : false, "type" : { "otype" : "PublicationType", "mtid" : 24, "link" : "/api/publicationtype/24", "label" : "Folyóiratcikk", "code" : 24, "otypeName" : "JournalArticle", "listPosition" : 1, "published" : true, "oldId" : 24, "snippet" : true }, "subType" : { "otype" : "SubType", "mtid" : 10000059, "link" : "/api/subtype/10000059", "label" : "Szakcikk (Folyóiratcikk)", "name" : "Szakcikk", "nameEng" : "Article", "docType" : { "otype" : "PublicationType", "mtid" : 24, "link" : "/api/publicationtype/24", "label" : "Folyóiratcikk", "code" : 24, "otypeName" : "JournalArticle", "listPosition" : 1, "published" : true, "oldId" : 24, "snippet" : true }, "listPosition" : 101, "published" : true, "oldId" : 10000059, "snippet" : true }, "category" : { "otype" : "Category", "mtid" : 1, "link" : "/api/category/1", "label" : "Tudományos", "published" : true, "oldId" : 1, "snippet" : true }, "languages" : [ { "otype" : "Language", "mtid" : 10002, "link" : "/api/language/10002", "label" : "Angol", "name" : "Angol", "nameEng" : "English", "published" : true, "oldId" : 2, "snippet" : true } ], "firstAuthor" : "Jeszenoi, N", "authorships" : [ { "otype" : "PersonAuthorship", "mtid" : 6192334, "link" : "/api/authorship/6192334", "label" : "Jeszenoi, N [Jeszenői, Norbert (Számítógépes kémi...), szerző]", "listPosition" : 1, "share" : 0.2, "first" : true, "last" : false, "author" : { "otype" : "Author", "mtid" : 10028233, "link" : "/api/author/10028233", "label" : "Jeszenői Norbert (Számítógépes kémia, gyógyszerkutatás)", "familyName" : "Jeszenői", "givenName" : "Norbert", "published" : true, "oldId" : 10028233, "snippet" : true }, "familyName" : "Jeszenoi", "givenName" : "N", "authorTyped" : true, "editorTyped" : false, "otherTyped" : false, "type" : { "otype" : "AuthorshipType", "mtid" : 1, "link" : "/api/authorshiptype/1", "label" : "Szerző", "code" : 0, "published" : true, "oldId" : 0, "snippet" : true }, "published" : false, "oldId" : 21413620, "snippet" : true }, { "otype" : "PersonAuthorship", "mtid" : 6192335, "link" : "/api/authorship/6192335", "label" : "Horvath, I [Horváth, István (Elméleti kémia), szerző] Kémia Doktori Iskola (SZTE / DI)", "listPosition" : 2, "share" : 0.2, "first" : false, "last" : false, "author" : { "otype" : "Author", "mtid" : 10052611, "link" : "/api/author/10052611", "label" : "Horváth István (Elméleti kémia)", "familyName" : "Horváth", "givenName" : "István", "published" : true, "oldId" : 10052611, "snippet" : true }, "familyName" : "Horvath", "givenName" : "I", "authorTyped" : true, "editorTyped" : false, "otherTyped" : false, "type" : { "otype" : "AuthorshipType", "mtid" : 1, "link" : "/api/authorshiptype/1", "label" : "Szerző", "code" : 0, "published" : true, "oldId" : 0, "snippet" : true }, "published" : false, "oldId" : 21413619, "snippet" : true }, { "otype" : "PersonAuthorship", "mtid" : 6192336, "link" : "/api/authorship/6192336", "label" : "Balint, M [Bálint, Mónika Enikő (Biokémia, Molekul...), szerző]", "listPosition" : 3, "share" : 0.2, "first" : false, "last" : false, "author" : { "otype" : "Author", "mtid" : 10044915, "link" : "/api/author/10044915", "label" : "Bálint Mónika Enikő (Biokémia, Molekuláris modellezés)", "familyName" : "Bálint", "givenName" : "Mónika Enikő", "published" : true, "oldId" : 10044915, "snippet" : true }, "familyName" : "Balint", "givenName" : "M", "authorTyped" : true, "editorTyped" : false, "otherTyped" : false, "type" : { "otype" : "AuthorshipType", "mtid" : 1, "link" : "/api/authorshiptype/1", "label" : "Szerző", "code" : 0, "published" : true, "oldId" : 0, "snippet" : true }, "published" : false, "oldId" : 21413618, "snippet" : true }, { "otype" : "PersonAuthorship", "mtid" : 6192337, "link" : "/api/authorship/6192337", "label" : "van der Spoel, D", "listPosition" : 4, "share" : 0.2, "first" : false, "last" : false, "familyName" : "van der Spoel", "givenName" : "D", "authorTyped" : true, "editorTyped" : false, "otherTyped" : false, "type" : { "otype" : "AuthorshipType", "mtid" : 1, "link" : "/api/authorshiptype/1", "label" : "Szerző", "code" : 0, "published" : true, "oldId" : 0, "snippet" : true }, "published" : false, "oldId" : 21413617, "snippet" : true }, { "otype" : "PersonAuthorship", "mtid" : 6192338, "link" : "/api/authorship/6192338", "label" : "Hetenyi, C ✉ [Hetényi, Csaba (Farmakoinformatik...), szerző] MTA-ELTE Molekuláris Biofizikai Kutatócsoport (ELTE / TTK / Bio_I)", "listPosition" : 5, "share" : 0.2, "first" : false, "last" : true, "corresponding" : true, "author" : { "otype" : "Author", "mtid" : 10001657, "link" : "/api/author/10001657", "label" : "Hetényi Csaba (Farmakoinformatika, molekulaszerkezet)", "familyName" : "Hetényi", "givenName" : "Csaba", "published" : true, "oldId" : 10001657, "snippet" : true }, "familyName" : "Hetenyi", "givenName" : "C", "authorTyped" : true, "editorTyped" : false, "otherTyped" : false, "type" : { "otype" : "AuthorshipType", "mtid" : 1, "link" : "/api/authorshiptype/1", "label" : "Szerző", "code" : 0, "published" : true, "oldId" : 0, "snippet" : true }, "published" : false, "oldId" : 21413616, "snippet" : true } ], "title" : "Mobility-based prediction of hydration structures of protein surfaces.", "identifiers" : [ { "otype" : "PublicationIdentifier", "mtid" : 964879, "link" : "/api/publicationidentifier/964879", "label" : "DOI: 10.1093/bioinformatics/btv093", "source" : { "otype" : "PlainSource", "mtid" : 6, "link" : "/api/publicationsource/6", "label" : "DOI", "type" : { "otype" : "PublicationSourceType", "mtid" : 10001, "link" : "/api/publicationsourcetype/10001", "label" : "DOI", "mayHaveOa" : true, "published" : true, "snippet" : true }, "name" : "DOI", "nameEng" : "DOI", "linkPattern" : "https://doi.org/@@@", "publiclyVisible" : true, "published" : true, "oldId" : 6, "snippet" : true }, "oaType" : "GOLD", "oaFree" : true, "validState" : "IDENTICAL", "idValue" : "10.1093/bioinformatics/btv093", "realUrl" : "https://doi.org/10.1093/bioinformatics/btv093", "published" : false, "oldId" : 1108536, "snippet" : true }, { "otype" : "PublicationIdentifier", "mtid" : 964877, "link" : "/api/publicationidentifier/964877", "label" : "WoS: 000356625700054", "source" : { "otype" : "PlainSource", "mtid" : 1, "link" : "/api/publicationsource/1", "label" : "WoS", "type" : { "otype" : "PublicationSourceType", "mtid" : 10003, "link" : "/api/publicationsourcetype/10003", "label" : "Indexelő adatbázis", "mayHaveOa" : false, "published" : true, "snippet" : true }, "name" : "WoS", "nameEng" : "WoS", "linkPattern" : "https://www.webofscience.com/wos/woscc/full-record/@@@", "publiclyVisible" : true, "published" : true, "oldId" : 1, "snippet" : true }, "oaFree" : false, "validState" : "IDENTICAL", "idValue" : "000356625700054", "realUrl" : "https://www.webofscience.com/wos/woscc/full-record/000356625700054", "published" : false, "oldId" : 1177079, "snippet" : true }, { "otype" : "PublicationIdentifier", "mtid" : 964878, "link" : "/api/publicationidentifier/964878", "label" : "Scopus: 84931046155", "source" : { "otype" : "PlainSource", "mtid" : 3, "link" : "/api/publicationsource/3", "label" : "Scopus", "type" : { "otype" : "PublicationSourceType", "mtid" : 10003, "link" : "/api/publicationsourcetype/10003", "label" : "Indexelő adatbázis", "mayHaveOa" : false, "published" : true, "snippet" : true }, "name" : "Scopus", "linkPattern" : "http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-@@@", "publiclyVisible" : true, "published" : true, "oldId" : 3, "snippet" : true }, "oaFree" : false, "validState" : "IDENTICAL", "idValue" : "84931046155", "realUrl" : "http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-84931046155", "published" : false, "oldId" : 1175237, "snippet" : true }, { "otype" : "PublicationIdentifier", "mtid" : 964880, "link" : "/api/publicationidentifier/964880", "label" : "PubMed: 25682067", "source" : { "otype" : "PlainSource", "mtid" : 17, "link" : "/api/publicationsource/17", "label" : "PubMed", "type" : { "otype" : "PublicationSourceType", "mtid" : 10003, "link" : "/api/publicationsourcetype/10003", "label" : "Indexelő adatbázis", "mayHaveOa" : false, "published" : true, "snippet" : true }, "name" : "PubMed", "nameEng" : "PubMed", "linkPattern" : "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=@@@&dopt=Abstract", "publiclyVisible" : true, "published" : true, "oldId" : 17, "snippet" : true }, "oaFree" : false, "validState" : "NO", "idValue" : "25682067", "realUrl" : "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=25682067&dopt=Abstract", "published" : false, "oldId" : 1108537, "snippet" : true } ], "journal" : { "otype" : "Journal", "mtid" : 16267, "link" : "/api/journal/16267", "label" : "BIOINFORMATICS 1367-4803 1460-2059", "pIssn" : "1367-4803", "eIssn" : "1460-2059", "reviewType" : "REVIEWED", "noIF" : false, "sciIndexed" : true, "scopusIndexed" : true, "lang" : "FOREIGN", "hungarian" : false, "published" : true, "oldId" : 16267, "snippet" : true }, "volume" : "31", "issue" : "12", "firstPage" : "1959", "lastPage" : "1965", "internalId" : "btv093", "firstPageOrInternalIdForSort" : "1959, btv093", "pageLength" : 7, "publishedYear" : 2015, "abstractText" : "MOTIVATION: Hydration largely determines solubility, aggregation of proteins and influences interactions between proteins and drug molecules. Despite the importance of hydration, structural determination of hydration structure of protein surfaces is still challenging from both experimental and theoretical viewpoints. The precision of experimental measurements is often affected by fluctuations and mobility of water molecules resulting in uncertain assignment of water positions. RESULTS: Our method can utilize mobility as an information source for the prediction of hydration structure. The necessary information can be produced by molecular dynamics simulations accounting for all atomic interactions including water-water contacts. The predictions were validated and tested by comparison to more than 1500 crystallographic water positions in twenty hydrated protein molecules including enzymes of biomedical importance such as cyclin-dependent kinase 2. The agreement with experimental water positions was larger than 80 % on average. The predictions can be particularly useful in situations where no or limited experimental knowledge is available on hydration structures of molecular surfaces. Availability and Implementation: The method is implemented in a standalone C program MobyWat released under the GNU General Public License, freely accessible with full documentation at {{http://www.mobywat.com}}. CONTACT: csabahete@yahoo.com SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.", "subjects" : [ { "otype" : "Classification", "mtid" : 10003, "link" : "/api/classification/10003", "label" : "Matematika", "published" : true, "snippet" : true }, { "otype" : "Classification", "mtid" : 10034, "link" : "/api/classification/10034", "label" : "Számítás- és információtudomány", "published" : true, "snippet" : true } ], "digital" : null, "printed" : null, "sourceYear" : 2015, "packet" : "636809", "foreignEdition" : true, "foreignLanguage" : true, "fullPublication" : true, "conferencePublication" : false, "nationalOrigin" : null, "missingAuthor" : false, "oaType" : "GOLD", "oaCheckDate" : "2024-02-17", "oaFree" : true, "oaLink" : "https://doi.org/10.1093/bioinformatics/btv093", "oaByAuthor" : { "otype" : "Admin", "mtid" : 10045349, "link" : "/api/admin/10045349", "label" : "Fekete Rita (PTE GYTK admin 5)", "familyName" : "Fekete", "givenName" : "Rita", "published" : true, "oldId" : 10045349, "snippet" : true }, "citationCount" : 27, "citationCountUnpublished" : 0, "citationCountWoOther" : 25, "independentCitCountWoOther" : 11, "nationalOriginCitationCount" : 13, "foreignEditionCitationCount" : 25, "doiCitationCount" : 27, "wosCitationCount" : 24, "scopusCitationCount" : 25, "wosScopusCitationCount" : 25, "wosScopusCitationCountWoOther" : 25, "wosScopusIndependentCitationCount" : 11, "wosScopusIndependentCitationCountWoOther" : 11, "independentCitationCount" : 11, "selfCitationCount" : 16, "unhandledCitationCount" : 0, "citingPubCount" : 27, "independentCitingPubCount" : 11, "citingPubCountWoOther" : 25, "independentCitingPubCountWoOther" : 11, "unhandledCitingPubCount" : 0, "citedPubCount" : 0, "citedCount" : 0, "pubStats" : { "types" : [ { "type" : "Folyóiratcikk", "typeEng" : "Journal Article", "code" : 24, "count" : 25 }, { "type" : "Könyvrészlet", "typeEng" : "Chapter in Book", "code" : 25, "count" : 0 }, { "type" : "Könyv", "typeEng" : "Book", "code" : 23, "count" : 0 }, { "type" : "Egyéb konferenciaközlemény", "typeEng" : "Conference paper", "code" : 31, "count" : 0 }, { "type" : "Egyéb konferenciakötet", "typeEng" : "Conference proceedings", "code" : 32, "count" : 0 }, { "type" : "Oltalmi formák", "typeEng" : "Protection forms", "code" : 26, "count" : 0 }, { "type" : "Disszertáció", "typeEng" : "Thesis", "code" : 28, "count" : 2 }, { "type" : "Egyéb", "typeEng" : "Miscellaneous", "code" : 29, "count" : 0 }, { "type" : "Alkotás", "typeEng" : "Achievement", "code" : 22, "count" : 0 }, { "type" : "Kutatási adat", "typeEng" : "Research data", "code" : 33, "count" : 0 } ], "citationTypes" : [ { "type" : "Folyóiratcikk", "typeEng" : "Journal Article", "code" : 24, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Könyvrészlet", "typeEng" : "Chapter in Book", "code" : 25, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Könyv", "typeEng" : "Book", "code" : 23, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Egyéb konferenciaközlemény", "typeEng" : "Conference paper", "code" : 31, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Egyéb konferenciakötet", "typeEng" : "Conference proceedings", "code" : 32, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Oltalmi formák", "typeEng" : "Protection forms", "code" : 26, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Disszertáció", "typeEng" : "Thesis", "code" : 28, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Egyéb", "typeEng" : "Miscellaneous", "code" : 29, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Alkotás", "typeEng" : "Achievement", "code" : 22, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 }, { "type" : "Kutatási adat", "typeEng" : "Research data", "code" : 33, "countUnknown" : 0, "countIndependent" : 0, "countSelfCitation" : 0 } ], "years" : [ { "year" : 2015, "publicationCount" : 0, "citationCount" : 1, "independentCitationCount" : 0, "citingPubCount" : 1, "independentCitingPubCount" : 0, "oaStats" : null, "oaStats2" : null }, { "year" : 2016, "publicationCount" : 0, "citationCount" : 2, "independentCitationCount" : 0, "citingPubCount" : 2, "independentCitingPubCount" : 0, "oaStats" : null, "oaStats2" : null }, { "year" : 2017, "publicationCount" : 0, "citationCount" : 5, "independentCitationCount" : 2, "citingPubCount" : 5, "independentCitingPubCount" : 2, "oaStats" : null, "oaStats2" : null }, { "year" : 2018, "publicationCount" : 0, "citationCount" : 4, "independentCitationCount" : 2, "citingPubCount" : 4, "independentCitingPubCount" : 2, "oaStats" : null, "oaStats2" : null }, { "year" : 2019, "publicationCount" : 0, "citationCount" : 2, "independentCitationCount" : 1, "citingPubCount" : 2, "independentCitingPubCount" : 1, "oaStats" : null, "oaStats2" : null }, { "year" : 2020, "publicationCount" : 0, "citationCount" : 3, "independentCitationCount" : 1, "citingPubCount" : 3, "independentCitingPubCount" : 1, "oaStats" : null, "oaStats2" : null }, { "year" : 2021, "publicationCount" : 0, "citationCount" : 2, "independentCitationCount" : 0, "citingPubCount" : 2, "independentCitingPubCount" : 0, "oaStats" : null, "oaStats2" : null }, { "year" : 2022, "publicationCount" : 0, "citationCount" : 4, "independentCitationCount" : 3, "citingPubCount" : 4, "independentCitingPubCount" : 3, "oaStats" : null, "oaStats2" : null }, { "year" : 2023, "publicationCount" : 0, "citationCount" : 4, "independentCitationCount" : 2, "citingPubCount" : 4, "independentCitingPubCount" : 2, "oaStats" : null, "oaStats2" : null } ] }, "ratings" : [ { "otype" : "SjrRating", "mtid" : 11007549, "link" : "/api/sjrrating/11007549", "label" : "sjr:D1 (2015) Scopus - Biochemistry BIOINFORMATICS 1367-4803 1460-2059", "listPos" : 15, "rankValue" : 0.1, "type" : "journal", "ratingType" : { "otype" : "RatingType", "mtid" : 10002, "link" : "/api/ratingtype/10002", "label" : "sjr", "code" : "sjr", "published" : true, "snippet" : true }, "subject" : { "otype" : "ClassificationExternal", "mtid" : 1303, "link" : "/api/classificationexternal/1303", "label" : "Scopus - Biochemistry", "published" : true, "oldId" : 1303, "snippet" : true }, "ranking" : "D1", "calculation" : "DIRECT", "published" : true, "snippet" : true } ], "ratingsForSort" : "D1", "references" : [ { "otype" : "Reference", "mtid" : 1979286, "link" : "/api/reference/1979286", "label" : "1. Abel, R., Role of the active-site solvent in the thermodynamics of factor Xa ligand binding (2008) J. Am. Chem. Soc, 130, pp. 2817-2831", "listPosition" : 1, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979287, "link" : "/api/reference/1979287", "label" : "2. Afonine, P.V., Bulk-solvent and overall scaling revisited: Faster calculations, improved results (2013) Acta Cryst., D69, pp. 625-634", "listPosition" : 2, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979288, "link" : "/api/reference/1979288", "label" : "3. Akli, S., Cdk2 is required for breast cancer mediated by the lowmolecular-weight isoform of Cyclin e (2011) Cancer Res, (71), pp. 3377-3386", "listPosition" : 3, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979289, "link" : "/api/reference/1979289", "label" : "4. Angel, T.E., Structural waters define a functional channel mediating activation of the GPCR rhodopsin (2009) Proc. Natl Acad. Sci. USA, 106, pp. 147367-214372", "listPosition" : 4, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979290, "link" : "/api/reference/1979290", "label" : "5. Antonyuk, S.V., Structures of protein-protein complexes involved in electron transfer (2013) Nature, (496), pp. 123-126", "listPosition" : 5, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979291, "link" : "/api/reference/1979291", "label" : "6. Badger, J., Modeling and refinement of water molecules and disordered solvent (1997) Methods Enzymol, 277, pp. 344-352", "listPosition" : 6, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979292, "link" : "/api/reference/1979292", "label" : "7. Baron, R., Hydrophobic association and volume-confined water molecules (2012) Protein-Ligand Interactions, , Gohlke, H. (ed. Wiley-VCH Verlag GmbH& Co. KGaA, Wennheim", "listPosition" : 7, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979293, "link" : "/api/reference/1979293", "label" : "8. Carugo, O., Correlation between occupancy and B-factor of water molecules in protein crystal structures (1999) Protein Eng, 12, pp. 1021-1024", "listPosition" : 8, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979294, "link" : "/api/reference/1979294", "label" : "9. Chenette, E.J., Senescence: A key role for CDK2 (2010) Nat. Rev. Cancer, (10), p. 84", "listPosition" : 9, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979295, "link" : "/api/reference/1979295", "label" : "10. Cheung, M.S., Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse (2002) Proc. Natl Acad. Sci. USA, 99, pp. 685-690", "listPosition" : 10, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979296, "link" : "/api/reference/1979296", "label" : "11. Cui, G., SPAM: A simple approach for profiling bound water molecules (2013) J. Chem. Theor. Comput, (9), pp. 5539-5549", "listPosition" : 11, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979297, "link" : "/api/reference/1979297", "label" : "12. De La Lande, A., Surface residues dynamically organize water bridges to enhance electron transfer between proteins (2010) Proc. Natl Acad. Sci. USA, (107), pp. 11799-11804", "listPosition" : 12, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979298, "link" : "/api/reference/1979298", "label" : "13. Dror, R.O., Biomolecular simulation: A computational microscope for molecular biology (2012) Annu. Rev. Biophys, (41), pp. 429-452", "listPosition" : 13, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979299, "link" : "/api/reference/1979299", "label" : "14. Ehrlich, L., Prediction of protein hydration sites from sequence by modular neural networks (1998) Protein Eng. Des. Sel, 11, pp. 11-19", "listPosition" : 14, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979300, "link" : "/api/reference/1979300", "label" : "15. Fang, C., Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy (2009) Nature, 462, pp. 200-204", "listPosition" : 15, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979301, "link" : "/api/reference/1979301", "label" : "16. Finney, J.L., The organization and function of water in protein crystals (1977) Philos. Trans. R. Soc. Lond. B, 278, pp. 3-32", "listPosition" : 16, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979302, "link" : "/api/reference/1979302", "label" : "17. García-Sosa, A.T., Hydration properties of ligands and drugs in protein binding sites: Tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies (2013) J. Chem. Inf. Model, (53), pp. 1388-1405", "listPosition" : 17, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979303, "link" : "/api/reference/1979303", "label" : "18. García-Sosa, A.T., WaterScore: A novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes (2003) J. Mol. Mod, 9, pp. 172-182", "listPosition" : 18, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979304, "link" : "/api/reference/1979304", "label" : "19. Garcia-Sosa, A.T., Including tightly-bound water molecules in de novo drug design Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands (2005) J. Chem. Inf. Model, 45, pp. 624-633", "listPosition" : 19, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979305, "link" : "/api/reference/1979305", "label" : "20. Garcia-Sosa, A.T., Mancera, R.L., The effect of tightly-bound water molecules on scaffold diversity in the computer-Aided de novo ligand design of CDK2 inhibitors (2006) J. Mol. Mod, 12, pp. 422-431", "listPosition" : 20, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979306, "link" : "/api/reference/1979306", "label" : "21. Halle, B., Protein hydration dynamics in solution: A critical survey (2004) Philos. Trans. R. Soc. Lond. B, 359, pp. 1207-1224", "listPosition" : 21, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979307, "link" : "/api/reference/1979307", "label" : "22. Halle, B., Biomolecular cryocrystallography: Structural changes during flash-cooling (2004) Proc. Natl Acad. Sci. USA, 101, pp. 4793-4798", "listPosition" : 22, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979308, "link" : "/api/reference/1979308", "label" : "23. Henchman, R.H., McCammon, J.A., Extracting hydration sites around proteins from explicit water simulations (2002) J. Comput. Chem, 23, pp. 861-869", "listPosition" : 23, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979309, "link" : "/api/reference/1979309", "label" : "24. Hess, B., GROMACS 4: Algorithms for highly efficient load-balanced, and scalable molecular simulation (2008) J. Chem. Theory Comput, 4, pp. 435-447", "listPosition" : 24, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979310, "link" : "/api/reference/1979310", "label" : "25. Israelachvili, J., Wennerstroam, H., Role of hydration and water structure in biological and colloidal interactions (1996) Nature, 379, pp. 219-225", "listPosition" : 25, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979311, "link" : "/api/reference/1979311", "label" : "26. Levy, Y., Onuchic, J.N., Water mediation in protein folding and molecular recognition (2006) Annu. Rev. Biophys. Biomol. Struct, 35, pp. 389-415", "listPosition" : 26, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979312, "link" : "/api/reference/1979312", "label" : "27. Lloyd, D.G., The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models (2004) J. Comput. Aided Mol. des, 18, pp. 89-100", "listPosition" : 27, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979313, "link" : "/api/reference/1979313", "label" : "28. Lopes, P.E.M., Polarizable force field for peptides and proteins based on the classical drude oscillator (2013) J. Chem. Theor. Comput, (9), pp. 5430-5449", "listPosition" : 28, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979314, "link" : "/api/reference/1979314", "label" : "29. Makarov, V.A., Reconstructing the protein-water interface (1998) Biopolymers, 45, pp. 469-478", "listPosition" : 29, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979315, "link" : "/api/reference/1979315", "label" : "30. Mancera, R.L., Molecular modeling of hydration in drug design (2007) Curr. Opin. Drug Discov. Dev, 10, pp. 275-280", "listPosition" : 30, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979316, "link" : "/api/reference/1979316", "label" : "31. Michel, J., Energetics of displacing water molecules from protein binding sites: Consequences for ligand optimization (2009) J. Am. Chem. Soc, 131, pp. 15403-15411", "listPosition" : 31, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979317, "link" : "/api/reference/1979317", "label" : "32. Nisius, L., Grzesiek, S., Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network (2012) Nat. Chem, (4), pp. 711-717", "listPosition" : 32, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979318, "link" : "/api/reference/1979318", "label" : "33. Patel, H., PyWATER: A PyMOL plug-in to find conserved water molecules in proteins by clustering (2014) Bioinformatics, (30), pp. 2978-2980", "listPosition" : 33, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979319, "link" : "/api/reference/1979319", "label" : "34. Petsko, G.A., Ringe, D., (2009) Protein Structure and Function, , Oxford University Press Inc., New York", "listPosition" : 34, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979320, "link" : "/api/reference/1979320", "label" : "35. Pettitt, B.M., Karplus, M., The structure of water surrounding a peptide: A theoretical approach (1987) Chem. Phys. Lett, (136), pp. 383-386", "listPosition" : 35, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979321, "link" : "/api/reference/1979321", "label" : "36. Pitt, W.R., Goodfellow, J.M., Modelling of solvent positions around polar groups in proteins (1991) Protein Eng, 4, pp. 531-537", "listPosition" : 36, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979322, "link" : "/api/reference/1979322", "label" : "37. Pronk, S., GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit (2013) Bioinformatics, (29), pp. 845-854", "listPosition" : 37, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979323, "link" : "/api/reference/1979323", "label" : "38. Roberts, B.C., Mancera, R.L., Ligand-protein docking with water molecules (2008) J. Chem. Inf. Model, 48, pp. 397-408", "listPosition" : 38, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979324, "link" : "/api/reference/1979324", "label" : "39. Ross, G.A., Rapid and accurate prediction and scoring of water molecules in protein binding sites (2012) PLoS ONE, (7), p. e32036", "listPosition" : 39, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979325, "link" : "/api/reference/1979325", "label" : "40. Savage, H., Wlodawer, A., Determination of water structure around biomolecules using x-ray and neutron diffraction methods (1986) Methods Enzymol, 127, pp. 162-183", "listPosition" : 40, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979326, "link" : "/api/reference/1979326", "label" : "41. Schoenborn, B.P., Hydration in protein crystallography (1995) Prog. Biophys. Mol. Biol, 64, pp. 105-119", "listPosition" : 41, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979327, "link" : "/api/reference/1979327", "label" : "42. Schulze-Gahmen, U., High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: Bound waters and natural ligand as guides for inhibitor design (1996) J. Med. Chem, 39, pp. 4540-4546", "listPosition" : 42, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979328, "link" : "/api/reference/1979328", "label" : "43. Schymkowitz, J.W.H., Prediction of water and metal binding sites and their affinities by using the Fold-X force field (2005) Proc. Natl Acad. Sci. USA, 102, pp. 10147-10152", "listPosition" : 43, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979329, "link" : "/api/reference/1979329", "label" : "44. Shan, Y., How does a drug molecule find its target binding site (2011) J Am. Chem. Soc, 133, pp. 9181-9183", "listPosition" : 44, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979330, "link" : "/api/reference/1979330", "label" : "45. Söderhjelm, P., Locating binding poses in protein-ligand systems using reconnaissance metadynamics (2012) Proc. Natl Acad. Sci. USA, (109), pp. 5170-5175", "listPosition" : 45, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979331, "link" : "/api/reference/1979331", "label" : "46. Thilagavathi, R., Mancera, R.L., Ligand-protein cross docking with water molecules (2010) J. Chem. Inf. Model, (50), pp. 415-421", "listPosition" : 46, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979332, "link" : "/api/reference/1979332", "label" : "47. Thirumalai, D., Role of water in protein aggregation and amyloid polymorphism (2011) Acc. Chem. Res, (45), pp. 83-92", "listPosition" : 47, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979333, "link" : "/api/reference/1979333", "label" : "48. Truchon, J.-F., A cavity corrected 3D-RISM functional for accurate solvation free energies (2014) J. Chem. Theor. Comput, (10), pp. 934-941", "listPosition" : 48, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979334, "link" : "/api/reference/1979334", "label" : "49. Van Der Spoel, D., Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media (2006) J. Phys. Chem. B, 110, pp. 4393-4398", "listPosition" : 49, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979335, "link" : "/api/reference/1979335", "label" : "50. Vedani, A., Huhta, D.W., An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds (1991) J. Am. Chem. Soc, 113, pp. 5860-5862", "listPosition" : 50, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979336, "link" : "/api/reference/1979336", "label" : "51. Virtanen, J.J., Modeling the hydration layer around proteins: HyPred (2010) Biophys. J., (99), pp. 1611-1619", "listPosition" : 51, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979337, "link" : "/api/reference/1979337", "label" : "52. Vogt, J., Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography (2000) Proteins, 41, pp. 545-553", "listPosition" : 52, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979338, "link" : "/api/reference/1979338", "label" : "53. Wu, B., Dong, D., Human cytosolic glutathione transferases: Structure, function, and drug discovery (2012) Trends Pharmacol. Sci, (33), pp. 656-668", "listPosition" : 53, "published" : false, "snippet" : true }, { "otype" : "Reference", "mtid" : 1979339, "link" : "/api/reference/1979339", "label" : "54. Xu, Y., Leitner, M.D., Vibrational energy flow through the green fluorescent protein-water interface: Communication maps and thermal boundary conductance (2014) J. Phys. Chem. B., (118), pp. 7818-7826", "listPosition" : 54, "published" : false, "snippet" : true } ], "hasCitationDuplums" : false, "inSelectedPubs" : "10044915", "userChangeableUntil" : "2015-07-14T11:27:09.000+0000", "publishDate" : "2015-03-22T22:00:21.000+0000", "directInstitutesForSort" : "Kémia Doktori Iskola (SZTE / DI); MTA-ELTE Molekuláris Biofizikai Kutatócsoport (ELTE / TTK / Bio_I)", "ownerAuthorCount" : 4, "ownerInstituteCount" : 23, "directInstituteCount" : 2, "authorCount" : 5, "contributorCount" : 0, "hasQualityFactor" : true, "link" : "/api/publication/2869502", "label" : "Jeszenoi N et al. Mobility-based prediction of hydration structures of protein surfaces.. (2015) BIOINFORMATICS 1367-4803 1460-2059 31 12 1959-1965", "template" : "