{"id":"https://openalex.org/W2059533496","doi":"https://doi.org/10.1142/s0219720008003588","title":"CONSERVED WATER MOLECULES IN X-RAY STRUCTURES HIGHLIGHT THE ROLE OF WATER IN INTRAMOLECULAR AND INTERMOLECULAR INTERACTIONS","display_name":"CONSERVED WATER MOLECULES IN X-RAY STRUCTURES HIGHLIGHT THE ROLE OF WATER IN INTRAMOLECULAR AND INTERMOLECULAR INTERACTIONS","publication_year":2008,"publication_date":"2008-08-01","ids":{"openalex":"https://openalex.org/W2059533496","doi":"https://doi.org/10.1142/s0219720008003588","mag":"2059533496","pmid":"https://pubmed.ncbi.nlm.nih.gov/18763742"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003588","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003588","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041482452","display_name":"Evgeniy Aksianov","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"EVGENIY AKSIANOV","raw_affiliation_strings":["A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046747242","display_name":"Olga Zanegina","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"OLGA ZANEGINA","raw_affiliation_strings":["Bioengineering and Bioinformatics Faculty, Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"Bioengineering and Bioinformatics Faculty, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001364639","display_name":"Grishin Av","orcid":"https://orcid.org/0000-0002-1436-9015"},"institutions":[{"id":"https://openalex.org/I3019350493","display_name":"Moscow State Agroengineering University named after V.P. Goryachkin","ror":"https://ror.org/02b4gv182","country_code":"RU","type":"education","lineage":["https://openalex.org/I3019350493"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"ALEXANDER GRISHIN","raw_affiliation_strings":["Russian State Agrarian University \u2013 Moscow Timiryazev Agricultural Academy, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"Russian State Agrarian University \u2013 Moscow Timiryazev Agricultural Academy, Moscow, Russia","institution_ids":["https://openalex.org/I3019350493"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076136987","display_name":"Sergey Spirin","orcid":"https://orcid.org/0000-0002-8041-1808"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"SERGEY SPIRIN","raw_affiliation_strings":["A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019487567","display_name":"A. S. Karyagina","orcid":"https://orcid.org/0000-0002-2580-3489"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"ANNA KARYAGINA","raw_affiliation_strings":["N.F. Gamaleya Research Institute of Epidemiology and Microbiology Institute of Agricultural Biotechnology, Russian Academy of Medical Sciences, Institute of Agricultural Biotechnology, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"N.F. Gamaleya Research Institute of Epidemiology and Microbiology Institute of Agricultural Biotechnology, Russian Academy of Medical Sciences, Institute of Agricultural Biotechnology, Moscow, Russia","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056758947","display_name":"Andrei V. Alexeevski","orcid":"https://orcid.org/0000-0001-7939-9939"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"ANDREI ALEXEEVSKI","raw_affiliation_strings":["A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5041482452"],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":0.1347,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.53926361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"06","issue":"04","first_page":"775","last_page":"788"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9818999767303467,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9818999767303467,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.98089998960495,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9761000275611877,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/intramolecular-force","display_name":"Intramolecular force","score":0.9419552087783813},{"id":"https://openalex.org/keywords/intermolecular-force","display_name":"Intermolecular force","score":0.8946247100830078},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.6933509111404419},{"id":"https://openalex.org/keywords/macromolecule","display_name":"Macromolecule","score":0.6547765731811523},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5124667286872864},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.4469640254974365},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.42184627056121826},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4110134541988373},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.3600982427597046},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3280327320098877},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.2451033592224121},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16806823015213013}],"concepts":[{"id":"https://openalex.org/C75079739","wikidata":"https://www.wikidata.org/wiki/Q1571801","display_name":"Intramolecular force","level":2,"score":0.9419552087783813},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.8946247100830078},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.6933509111404419},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.6547765731811523},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5124667286872864},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4469640254974365},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.42184627056121826},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4110134541988373},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3600982427597046},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3280327320098877},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2451033592224121},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16806823015213013},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720008003588","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003588","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:18763742","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18763742","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.8500000238418579,"display_name":"Clean water and sanitation"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W39527118","https://openalex.org/W1484092314","https://openalex.org/W1564972078","https://openalex.org/W1964556609","https://openalex.org/W1964981581","https://openalex.org/W1976773992","https://openalex.org/W2003952807","https://openalex.org/W2026258231","https://openalex.org/W2028375832","https://openalex.org/W2062393124","https://openalex.org/W2065057333","https://openalex.org/W2085277871","https://openalex.org/W2090338420","https://openalex.org/W2103080667","https://openalex.org/W2131758362","https://openalex.org/W2144998676","https://openalex.org/W2164646439","https://openalex.org/W2414326370"],"related_works":["https://openalex.org/W2006004926","https://openalex.org/W2049231603","https://openalex.org/W781020412","https://openalex.org/W4361987403","https://openalex.org/W2014749179","https://openalex.org/W2002573755","https://openalex.org/W2054022363","https://openalex.org/W2057833269","https://openalex.org/W1995748575","https://openalex.org/W3035402709"],"abstract_inverted_index":{"Water":[0],"molecules":[1,36,107],"immobilized":[2],"on":[3,37],"a":[4,62,82],"protein":[5,39],"or":[6,70],"DNA":[7],"surface":[8],"are":[9],"known":[10],"to":[11,29,77,102],"play":[12],"an":[13],"important":[14],"role":[15],"in":[16,56,61,81,108,116],"intramolecular":[17,121],"and":[18,44,120],"intermolecular":[19,117],"interactions.":[20,125],"Comparative":[21],"analysis":[22],"of":[23,33,64,67,96],"related":[24,68],"three-dimensional":[25],"(3D)":[26],"structures":[27,66],"allows":[28],"predict":[30,103],"the":[31,38,46,58,89],"locations":[32],"such":[34],"water":[35,51,106],"surface.":[40],"We":[41],"have":[42],"developed":[43],"implemented":[45],"algorithm":[47,87],"WLAKE":[48,99],"detecting":[49],"\"conserved\"":[50],"molecules,":[52],"i.e.":[53],"those":[54],"located":[55],"almost":[57],"same":[59],"positions":[60],"set":[63],"superimposed":[65,97],"proteins":[69],"macromolecular":[71],"complexes.":[72],"The":[73,126],"problem":[74],"is":[75,128],"reduced":[76],"finding":[78],"maximal":[79],"cliques":[80],"certain":[83],"graph.":[84],"Despite":[85],"exponential":[86],"complexity,":[88],"program":[90,127],"works":[91],"appropriately":[92],"fast":[93],"for":[94],"dozens":[95],"structures.":[98],"was":[100],"used":[101],"functionally":[104],"significant":[105],"enzyme":[109],"active":[110],"sites":[111],"(transketolases)":[112],"as":[113,115],"well":[114],"(ETS-DNA":[118],"complexes)":[119],"(thiol-disulfide":[122],"interchange":[123],"protein)":[124],"available":[129],"online":[130],"at":[131],"http://monkey.belozersky.msu.ru/~evgeniy/wLake/wLake.html.":[132]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
