{"id":"https://openalex.org/W2075409132","doi":"https://doi.org/10.1016/j.jmgm.2005.05.002","title":"Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA","display_name":"Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA","publication_year":2005,"publication_date":"2005-06-29","ids":{"openalex":"https://openalex.org/W2075409132","doi":"https://doi.org/10.1016/j.jmgm.2005.05.002","mag":"2075409132","pmid":"https://pubmed.ncbi.nlm.nih.gov/15990344"},"language":"en","primary_location":{"id":"doi:10.1016/j.jmgm.2005.05.002","doi":"https://doi.org/10.1016/j.jmgm.2005.05.002","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jmgm.2005.05.002","pdf_url":null,"source":{"id":"https://openalex.org/S76694907","display_name":"Journal of Molecular Graphics and Modelling","issn_l":"1093-3263","issn":["1093-3263","1873-4243"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Graphics and Modelling","raw_type":"journal-article"},"volume":null,"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/A5012731226","display_name":"Adam D. Schuyler","orcid":"https://orcid.org/0000-0001-7583-899X","observed_orcids":["https://orcid.org/0000-0001-7583-899X"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam D. Schuyler","raw_affiliation_strings":["Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA","Department of Mechanical Engineering, The Johns Hopkins University, 223 Latrobe Hall, 3400 North Charles Street, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Mechanical Engineering, The Johns Hopkins University, 223 Latrobe Hall, 3400 North Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012775344","display_name":"Gregory S. Chirikjian","orcid":"https://orcid.org/0000-0003-0542-9028","observed_orcids":["https://orcid.org/0000-0003-0542-9028"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gregory S. Chirikjian","raw_affiliation_strings":["Department of Mechanical Engineering, The Johns Hopkins University, 223 Latrobe Hall, 3400 North Charles Street, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, The Johns Hopkins University, 223 Latrobe Hall, 3400 North Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012775344"],"corresponding_institution_ids":["https://openalex.org/I145311948"],"apc_list":{"value":3940,"currency":"USD","value_usd":3940},"apc_paid":null,"fwci":0.9329,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.70283383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"46","last_page":"58"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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":0.0,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/normal-mode-analysis","display_name":"normal mode analysis","score":0.8180000185966492},{"id":"https://openalex.org/keywords/harmonic-potential","display_name":"harmonic potential","score":0.8569999933242798},{"id":"https://openalex.org/keywords/structure-function-relationship","display_name":"structure-function relationship","score":0.6909999847412109},{"id":"https://openalex.org/keywords/conformational-pathways","display_name":"conformational pathways","score":0.8389999866485596},{"id":"https://openalex.org/keywords/computational-efficiency","display_name":"computational efficiency","score":0.6290000081062317},{"id":"https://openalex.org/keywords/mode-shapes","display_name":"mode shapes","score":0.7049999833106995}],"concepts":[{"id":"https://openalex.org/C32758168","wikidata":"https://www.wikidata.org/wiki/Q900488","display_name":"Normal mode","level":3,"score":0.6582319736480713},{"id":"https://openalex.org/C129844170","wikidata":"https://www.wikidata.org/wiki/Q41299","display_name":"Quadratic equation","level":2,"score":0.5996811389923096},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5955713391304016},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5801318287849426},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.5704806447029114},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5500034093856812},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5164154171943665},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5101628303527832},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4790278971195221},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4574129283428192},{"id":"https://openalex.org/C208081375","wikidata":"https://www.wikidata.org/wiki/Q274502","display_name":"Degrees of freedom (physics and chemistry)","level":2,"score":0.4341890215873718},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.4258652329444885},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2512379288673401},{"id":"https://openalex.org/C198394728","wikidata":"https://www.wikidata.org/wiki/Q3695508","display_name":"Vibration","level":2,"score":0.19806811213493347},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19584447145462036},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11221697926521301},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.10835051536560059},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08472093939781189},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1016/j.jmgm.2005.05.002","doi":"https://doi.org/10.1016/j.jmgm.2005.05.002","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jmgm.2005.05.002","pdf_url":null,"source":{"id":"https://openalex.org/S76694907","display_name":"Journal of Molecular Graphics and Modelling","issn_l":"1093-3263","issn":["1093-3263","1873-4243"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Molecular Graphics and Modelling","raw_type":"journal-article"},{"id":"pmid:15990344","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15990344","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,"listed_in":[],"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 molecular graphics & modelling","raw_type":"Comparative Study"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1499440913","https://openalex.org/W1892996896","https://openalex.org/W1965838279","https://openalex.org/W1966379257","https://openalex.org/W1967493918","https://openalex.org/W1968407616","https://openalex.org/W1981099976","https://openalex.org/W1985581342","https://openalex.org/W1995802556","https://openalex.org/W1998980954","https://openalex.org/W2007832948","https://openalex.org/W2021646539","https://openalex.org/W2032702737","https://openalex.org/W2034881955","https://openalex.org/W2044877050","https://openalex.org/W2057228803","https://openalex.org/W2062019978","https://openalex.org/W2066677535","https://openalex.org/W2069636465","https://openalex.org/W2075642255","https://openalex.org/W2078320842","https://openalex.org/W2082462938","https://openalex.org/W2084631697","https://openalex.org/W2101017457","https://openalex.org/W2102449622","https://openalex.org/W2106988671","https://openalex.org/W2108700551","https://openalex.org/W2112374350","https://openalex.org/W2113994268","https://openalex.org/W2131209038","https://openalex.org/W2131823126","https://openalex.org/W2132589721","https://openalex.org/W2136705807","https://openalex.org/W2142338805","https://openalex.org/W2147753319","https://openalex.org/W2151759496","https://openalex.org/W2153331570","https://openalex.org/W2156115459"],"related_works":["https://openalex.org/W7101214697","https://openalex.org/W2084631697","https://openalex.org/W2527704868","https://openalex.org/W2110947845","https://openalex.org/W4302065803","https://openalex.org/W2972989614","https://openalex.org/W4285272870","https://openalex.org/W2026035062","https://openalex.org/W2102211745","https://openalex.org/W2112315506"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}