{"id":"https://openalex.org/W3173559070","doi":"https://doi.org/10.3390/sym13071193","title":"Use of the Molecular Dynamics Method to Investigate the Stability of \u03b1-\u03b1-Corner Structural Motifs in Proteins","display_name":"Use of the Molecular Dynamics Method to Investigate the Stability of \u03b1-\u03b1-Corner Structural Motifs in Proteins","publication_year":2021,"publication_date":"2021-07-02","ids":{"openalex":"https://openalex.org/W3173559070","doi":"https://doi.org/10.3390/sym13071193","mag":"3173559070"},"language":"en","primary_location":{"id":"doi:10.3390/sym13071193","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13071193","pdf_url":"https://www.mdpi.com/2073-8994/13/7/1193/pdf?version=1625220201","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2073-8994/13/7/1193/pdf?version=1625220201","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038996145","display_name":"Vladimir R. Rudnev","orcid":"https://orcid.org/0000-0001-9618-346X"},"institutions":[{"id":"https://openalex.org/I4210088122","display_name":"Institute of Theoretical and Experimental Biophysics","ror":"https://ror.org/008ebms37","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210088122","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210152028","display_name":"Institute of Biomedical Chemistry","ror":"https://ror.org/040wrkp27","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210110862","https://openalex.org/I4210152028"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vladimir R. Rudnev","raw_affiliation_strings":["Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia","V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I4210088122"]},{"raw_affiliation_string":"V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia","institution_ids":["https://openalex.org/I4210152028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058479064","display_name":"Liudmila I. Kulikova","orcid":"https://orcid.org/0000-0002-7293-1504"},"institutions":[{"id":"https://openalex.org/I4210088122","display_name":"Institute of Theoretical and Experimental Biophysics","ror":"https://ror.org/008ebms37","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210088122","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210159227","display_name":"Institute of Mathematical Problems of Biology","ror":"https://ror.org/04xtpdj18","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210124601","https://openalex.org/I4210159227"]},{"id":"https://openalex.org/I86427540","display_name":"Keldysh Institute of Applied Mathematics","ror":"https://ror.org/01dv3hq14","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210124601","https://openalex.org/I86427540"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Liudmila I. Kulikova","raw_affiliation_strings":["Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia","Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I86427540","https://openalex.org/I4210159227"]},{"raw_affiliation_string":"Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I4210088122"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003500932","display_name":"Anna L. Kaysheva","orcid":"https://orcid.org/0000-0003-4472-2016"},"institutions":[{"id":"https://openalex.org/I4210152028","display_name":"Institute of Biomedical Chemistry","ror":"https://ror.org/040wrkp27","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210110862","https://openalex.org/I4210152028"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Anna L. Kaysheva","raw_affiliation_strings":["V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"V.N. Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia","institution_ids":["https://openalex.org/I4210152028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064884281","display_name":"\u0410. \u0412. \u0415\u0444\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0002-9539-270X"},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander V. Efimov","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I4210137602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077524727","display_name":"D. A. Tikhonov","orcid":"https://orcid.org/0000-0002-1779-464X"},"institutions":[{"id":"https://openalex.org/I4210088122","display_name":"Institute of Theoretical and Experimental Biophysics","ror":"https://ror.org/008ebms37","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210088122","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210159227","display_name":"Institute of Mathematical Problems of Biology","ror":"https://ror.org/04xtpdj18","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210124601","https://openalex.org/I4210159227"]},{"id":"https://openalex.org/I86427540","display_name":"Keldysh Institute of Applied Mathematics","ror":"https://ror.org/01dv3hq14","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210124601","https://openalex.org/I86427540"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitry A. Tikhonov","raw_affiliation_strings":["Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia","Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia"],"raw_orcid":"https://orcid.org/0000-0002-1779-464X","affiliations":[{"raw_affiliation_string":"Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I86427540","https://openalex.org/I4210159227"]},{"raw_affiliation_string":"Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia","institution_ids":["https://openalex.org/I4210088122"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5003500932"],"corresponding_institution_ids":["https://openalex.org/I4210152028"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.5551,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.63362887,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":"13","issue":"7","first_page":"1193","last_page":"1193"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9975000023841858,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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/molecular-dynamics","display_name":"Molecular dynamics","score":0.8058768510818481},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.7112435102462769},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.6158344745635986},{"id":"https://openalex.org/keywords/structural-stability","display_name":"Structural stability","score":0.5364267230033875},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38718268275260925},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.3866530656814575},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.32077062129974365},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3161389231681824},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2849994897842407},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22454962134361267},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.20712995529174805},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.19089791178703308},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14116206765174866},{"id":"https://openalex.org/keywords/structural-engineering","display_name":"Structural engineering","score":0.08102744817733765},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.06582716107368469}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.8058768510818481},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.7112435102462769},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.6158344745635986},{"id":"https://openalex.org/C155673373","wikidata":"https://www.wikidata.org/wiki/Q1648886","display_name":"Structural stability","level":2,"score":0.5364267230033875},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38718268275260925},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.3866530656814575},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32077062129974365},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3161389231681824},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2849994897842407},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22454962134361267},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.20712995529174805},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.19089791178703308},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14116206765174866},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.08102744817733765},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.06582716107368469},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/sym13071193","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13071193","pdf_url":"https://www.mdpi.com/2073-8994/13/7/1193/pdf?version=1625220201","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:f96ace64898b45a4aa8c9c0290fdcbc9","is_oa":true,"landing_page_url":"https://doaj.org/article/f96ace64898b45a4aa8c9c0290fdcbc9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symmetry, Vol 13, Iss 7, p 1193 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2073-8994/13/7/1193/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/sym13071193","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symmetry","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/sym13071193","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13071193","pdf_url":"https://www.mdpi.com/2073-8994/13/7/1193/pdf?version=1625220201","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","score":0.8100000023841858,"display_name":"Life below water"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3173559070.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W20098439","https://openalex.org/W1976499671","https://openalex.org/W2008708467","https://openalex.org/W2033159891","https://openalex.org/W2065762664","https://openalex.org/W2069123478","https://openalex.org/W2087272378","https://openalex.org/W2094087249","https://openalex.org/W2118233996","https://openalex.org/W2130479394","https://openalex.org/W2137967110","https://openalex.org/W2139308282","https://openalex.org/W2317126352","https://openalex.org/W2329837538","https://openalex.org/W2330113154","https://openalex.org/W2555525603","https://openalex.org/W2590478725","https://openalex.org/W3022095067","https://openalex.org/W3041213255","https://openalex.org/W4251056860","https://openalex.org/W4252395482"],"related_works":["https://openalex.org/W2128884622","https://openalex.org/W2112380088","https://openalex.org/W1715467939","https://openalex.org/W4318816969","https://openalex.org/W2161756346","https://openalex.org/W1977613337","https://openalex.org/W2075921262","https://openalex.org/W2300182960","https://openalex.org/W2338444630","https://openalex.org/W1990619265"],"abstract_inverted_index":{"This":[0],"study":[1],"investigated":[2,45],"the":[3,29,32,36,46,56,63,81,86,90,97],"stability":[4],"of":[5,25,48,60,62,72,89],"structural":[6,49],"motifs":[7,50],"via":[8],"molecular":[9,17,41,91,98],"dynamics,":[10],"using":[11],"\u03b1-\u03b1-corners":[12,26,101],"as":[13],"an":[14],"example.":[15],"A":[16],"dynamics":[18,42,92,99],"experiment":[19],"was":[20],"performed":[21],"on":[22],"a":[23,40],"sample":[24],"selected":[27],"by":[28,51],"authors":[30],"from":[31],"PDB":[33],"database.":[34],"For":[35],"first":[37],"time":[38],"during":[39],"experiment,":[43],"we":[44],"characteristics":[47],"describing":[52],"their":[53],"geometry,":[54],"including":[55],"interplanar":[57],"distance,":[58],"area":[59],"polygon":[61],"helices":[64,73],"projections":[65],"intersection,":[66],"and":[67],"torsion":[68,78],"angles":[69,79],"between":[70],"axes":[71],"in":[74,85,111],"helical":[75],"pairs.":[76],"The":[77],"for":[80],"constriction":[82],"amino":[83],"acids":[84],"equilibrium":[87],"portion":[88],"trajectory":[93],"were":[94,102],"analyzed.":[95],"Using":[96],"method,":[100],"found":[103],"to":[104],"be":[105],"autonomous":[106],"structures":[107],"that":[108],"are":[109],"stable":[110],"aquatic":[112],"environments.":[113]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}