{"id":"https://openalex.org/W4389934074","doi":"https://doi.org/10.1093/bioinformatics/btad761","title":"pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells","display_name":"pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells","publication_year":2023,"publication_date":"2023-12-15","ids":{"openalex":"https://openalex.org/W4389934074","doi":"https://doi.org/10.1093/bioinformatics/btad761","pmid":"https://pubmed.ncbi.nlm.nih.gov/38113434"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/1/btad761/55612866/btad761.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/1/btad761/55612866/btad761.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064409858","display_name":"Colin Brown","orcid":"https://orcid.org/0000-0002-5678-2799"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin Brown","raw_affiliation_strings":["Department of Physics, San Diego State University , San Diego, CA 92116, United States","Viral Information Institute, San Diego State University , San Diego, CA 92116, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Viral Information Institute, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091609101","display_name":"Anu Agarwal","orcid":"https://orcid.org/0000-0001-5264-1123"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anuradha Agarwal","raw_affiliation_strings":["Computational Science Research Center, San Diego State University , San Diego, CA 92116, United States","Viral Information Institute, San Diego State University , San Diego, CA 92116, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science Research Center, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Viral Information Institute, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086012925","display_name":"Antoni Luque","orcid":"https://orcid.org/0000-0002-5817-4914"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Antoni Luque","raw_affiliation_strings":["Computational Science Research Center, San Diego State University , San Diego, CA 92116, United States","Department of Biology, University of Miami , Coral Gables, FL 33146, United States","Department of Mathematics and Statistics, San Diego State University , San Diego, CA 92116, United States","Viral Information Institute, San Diego State University , San Diego, CA 92116, United States"],"raw_orcid":"https://orcid.org/0000-0002-5817-4914","affiliations":[{"raw_affiliation_string":"Computational Science Research Center, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Department of Biology, University of Miami , Coral Gables, FL 33146, United States","institution_ids":["https://openalex.org/I145608581"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Viral Information Institute, San Diego State University , San Diego, CA 92116, United States","institution_ids":["https://openalex.org/I26538001"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.915,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.76945036,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"40","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9764000177383423,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9764000177383423,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.0044999998062849045,"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":0.002400000113993883,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.600929319858551},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4541546404361725},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.438043475151062},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3969038426876068},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.39578625559806824},{"id":"https://openalex.org/keywords/structural-engineering","display_name":"Structural engineering","score":0.3253181278705597},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3205549716949463},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2845008671283722},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.2167542576789856},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20589303970336914},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1710512936115265},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.12536963820457458},{"id":"https://openalex.org/keywords/acoustics","display_name":"Acoustics","score":0.09673610329627991}],"concepts":[{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.600929319858551},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4541546404361725},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.438043475151062},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3969038426876068},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.39578625559806824},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.3253181278705597},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3205549716949463},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2845008671283722},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2167542576789856},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20589303970336914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1710512936115265},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.12536963820457458},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.09673610329627991}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/1/btad761/55612866/btad761.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38113434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38113434","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10786678","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10786678","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10786678/pdf/btad761.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/1/btad761/55612866/btad761.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1777582841","display_name":"Exploring the Origin of Viruses","funder_award_id":"GBMF9871","funder_id":"https://openalex.org/F4320306202","funder_display_name":"Gordon and Betty Moore Foundation"},{"id":"https://openalex.org/G2139452628","display_name":"CC* Storage: Implementation of a Distributed, Shareable, and Parallel Storage Resource at San Diego State University to Facilitate High-Performance Computing for Climate Science","funder_award_id":"1659169","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4215564400","display_name":null,"funder_award_id":"1951678","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389934074.pdf"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W104429531","https://openalex.org/W1594922720","https://openalex.org/W1976428836","https://openalex.org/W1982569826","https://openalex.org/W1991327427","https://openalex.org/W1991762941","https://openalex.org/W1994628856","https://openalex.org/W2032078921","https://openalex.org/W2076147133","https://openalex.org/W2078646305","https://openalex.org/W2087284052","https://openalex.org/W2089245650","https://openalex.org/W2113971181","https://openalex.org/W2120580263","https://openalex.org/W2130479394","https://openalex.org/W2142595184","https://openalex.org/W2148273034","https://openalex.org/W2148931575","https://openalex.org/W2152863535","https://openalex.org/W2155451445","https://openalex.org/W2166561873","https://openalex.org/W2169559165","https://openalex.org/W2554712729","https://openalex.org/W2738606079","https://openalex.org/W2766537900","https://openalex.org/W2772094206","https://openalex.org/W2772099288","https://openalex.org/W2791628793","https://openalex.org/W2800650932","https://openalex.org/W2809302218","https://openalex.org/W2893348872","https://openalex.org/W2926076572","https://openalex.org/W2950776490","https://openalex.org/W2962608495","https://openalex.org/W2975401555","https://openalex.org/W2977490236","https://openalex.org/W3005146385","https://openalex.org/W3010072931","https://openalex.org/W3010429656","https://openalex.org/W3016070378","https://openalex.org/W3035719236","https://openalex.org/W3080275484","https://openalex.org/W3083406432","https://openalex.org/W3087088531","https://openalex.org/W3095328467","https://openalex.org/W3113578674","https://openalex.org/W3119052201","https://openalex.org/W3135414395","https://openalex.org/W3136584239","https://openalex.org/W3137338205","https://openalex.org/W3140562424","https://openalex.org/W3153377878","https://openalex.org/W3161192779","https://openalex.org/W3181264219","https://openalex.org/W3202839349","https://openalex.org/W4200364132","https://openalex.org/W4200433935","https://openalex.org/W4200512963","https://openalex.org/W4206455287","https://openalex.org/W4220717330","https://openalex.org/W4224303521","https://openalex.org/W4226031774","https://openalex.org/W4242206406","https://openalex.org/W4281790889","https://openalex.org/W4283835959","https://openalex.org/W4294339123","https://openalex.org/W4304731451","https://openalex.org/W4362705771"],"related_works":["https://openalex.org/W1773535258","https://openalex.org/W2772226369","https://openalex.org/W1995820742","https://openalex.org/W4302334050","https://openalex.org/W2894584668","https://openalex.org/W4381082351","https://openalex.org/W4290020623","https://openalex.org/W2041396722","https://openalex.org/W4231106754","https://openalex.org/W2945562222"],"abstract_inverted_index":{"SUMMARY:":[0],"pyCapsid":[1,50,81,147,155,177],"is":[2,99,107,148],"a":[3,47,87,143,151],"Python":[4,110,119],"package":[5,26],"developed":[6,28],"to":[7,31,75],"facilitate":[8],"the":[9,12,32,52,65,68,72,76,83,132,137,163,169,179],"characterization":[10],"of":[11,18,35,40,55,67,146],"dynamics":[13],"and":[14,21,70,112,123,127,135,161,166],"quasi-rigid":[15,60],"mechanical":[16,61],"units":[17],"protein":[19,23,48],"shells":[20],"other":[22],"complexes.":[24],"The":[25],"was":[27],"in":[29,86,116,131,136,178],"response":[30],"rapid":[33],"increase":[34],"high-resolution":[36],"structures,":[37],"particularly":[38],"capsids":[39],"viruses,":[41],"requiring":[42],"multiscale":[43],"biophysical":[44],"analyses.":[45],"Given":[46],"shell,":[49],"generates":[51,162],"collective":[53],"vibrations":[54],"its":[56],"amino-acid":[57],"residues,":[58],"identifies":[59],"regions":[62],"associated":[63],"with":[64,109],"disassembly":[66],"structure,":[69],"maps":[71],"results":[73,85],"back":[74],"input":[77],"proteins":[78],"for":[79],"interpretation.":[80],"summarizes":[82],"main":[84],"report":[88,165],"that":[89],"includes":[90],"publication-quality":[91],"figures.":[92],"AVAILABILITY":[93],"AND":[94],"IMPLEMENTATION:":[95],"pyCapsid's":[96,138],"source":[97],"code":[98],"available":[100,130,149],"under":[101],"MIT":[102],"License":[103],"on":[104],"GitHub.":[105],"It":[106],"compatible":[108],"3.8-3.10":[111],"has":[113],"been":[114],"deployed":[115],"two":[117],"leading":[118],"package-management":[120],"systems,":[121],"PIP":[122],"Conda.":[124],"Installation":[125],"instructions":[126],"tutorials":[128],"are":[129],"online":[133],"documentation":[134],"YouTube":[139],"playlist.":[140],"In":[141],"addition,":[142],"cloud-based":[144],"implementation":[145],"as":[150,168],"Google":[152],"Colab":[153,156],"notebook.":[154],"does":[157],"not":[158],"require":[159],"installation":[160],"same":[164],"outputs":[167],"installable":[170],"version.":[171],"Users":[172],"can":[173],"post":[174],"issues":[175,181],"regarding":[176],"repository's":[180],"section.":[182]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
