{"id":"https://openalex.org/W3014576393","doi":"https://doi.org/10.1093/bioinformatics/btaa234","title":"FASPR: an open-source tool for fast and accurate protein side-chain packing","display_name":"FASPR: an open-source tool for fast and accurate protein side-chain packing","publication_year":2020,"publication_date":"2020-04-01","ids":{"openalex":"https://openalex.org/W3014576393","doi":"https://doi.org/10.1093/bioinformatics/btaa234","mag":"3014576393","pmid":"https://pubmed.ncbi.nlm.nih.gov/32259206"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa234","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/12/3758/33437211/btaa234.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/12/3758/33437211/btaa234.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072178740","display_name":"Xiaoqiang Huang","orcid":"https://orcid.org/0000-0002-1005-848X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaoqiang Huang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics"],"raw_orcid":"https://orcid.org/0000-0002-1005-848X","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015867959","display_name":"Robin Pearce","orcid":"https://orcid.org/0000-0001-6402-734X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robin Pearce","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Biological Chemistry , University of Michigan, Ann Arbor, MI 48109, USA","Department of Computational Medicine and Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry , University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100354659"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.8843,"has_fulltext":false,"cited_by_count":112,"citation_normalized_percentile":{"value":0.94966734,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"36","issue":"12","first_page":"3758","last_page":"3765"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.84579998254776,"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":0.84579998254776,"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":0.06459999829530716,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.03530000150203705,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.7136476039886475},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.572109580039978},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5587121844291687},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5125855803489685},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5102503299713135},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45027321577072144},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4413146376609802},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4229007363319397},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.28035807609558105},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.11948034167289734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10548755526542664},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09752359986305237}],"concepts":[{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.7136476039886475},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.572109580039978},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5587121844291687},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5125855803489685},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5102503299713135},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45027321577072144},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4413146376609802},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4229007363319397},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28035807609558105},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.11948034167289734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10548755526542664},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09752359986305237},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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/btaa234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa234","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/12/3758/33437211/btaa234.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32259206","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32259206","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:7320614","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7320614","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa234","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa234","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/12/3758/33437211/btaa234.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1492122016","display_name":"III: Medium: Collaborative Research: Multi-level computational approaches to protein function prediction","funder_award_id":"1901191","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G155194203","display_name":null,"funder_award_id":"R01 GM116960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1556211573","display_name":null,"funder_award_id":"GM-083107","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1815782265","display_name":null,"funder_award_id":"R01GM083107","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4509968318","display_name":null,"funder_award_id":"R01 AI134678","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G553838990","display_name":null,"funder_award_id":"GM116960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6840103790","display_name":"Collaborative Research: ABI Development: Integrated platforms for protein structure and function predictions","funder_award_id":"1564756","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8702286652","display_name":null,"funder_award_id":"AI134678","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1970157506","https://openalex.org/W1972728295","https://openalex.org/W1974130578","https://openalex.org/W1975338077","https://openalex.org/W1987134040","https://openalex.org/W2006192061","https://openalex.org/W2011658408","https://openalex.org/W2015403140","https://openalex.org/W2020530495","https://openalex.org/W2025221718","https://openalex.org/W2037312364","https://openalex.org/W2043010716","https://openalex.org/W2043701535","https://openalex.org/W2047544230","https://openalex.org/W2051203581","https://openalex.org/W2082221689","https://openalex.org/W2092087990","https://openalex.org/W2096536472","https://openalex.org/W2097891553","https://openalex.org/W2101569554","https://openalex.org/W2101712920","https://openalex.org/W2102516512","https://openalex.org/W2104078482","https://openalex.org/W2106648157","https://openalex.org/W2115540209","https://openalex.org/W2116275717","https://openalex.org/W2118233996","https://openalex.org/W2139040839","https://openalex.org/W2140248032","https://openalex.org/W2141685906","https://openalex.org/W2145778523","https://openalex.org/W2149669793","https://openalex.org/W2152107372","https://openalex.org/W2155636968","https://openalex.org/W2164130591","https://openalex.org/W2164750034","https://openalex.org/W2172114588","https://openalex.org/W2409199570","https://openalex.org/W2514016200","https://openalex.org/W2556222602","https://openalex.org/W2624773820","https://openalex.org/W2901818893","https://openalex.org/W2907676659","https://openalex.org/W2920919814","https://openalex.org/W2954253694","https://openalex.org/W2967586821","https://openalex.org/W2979549406","https://openalex.org/W2994942809","https://openalex.org/W6725919666"],"related_works":["https://openalex.org/W2279302736","https://openalex.org/W2802316666","https://openalex.org/W4280529929","https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"structure":[2,29,228],"and":[3,31,43,59,89,94,132,140,185,210,230,242,249],"function":[4,67],"are":[5,49,244,255],"essentially":[6],"determined":[7],"by":[8,62,109],"how":[9],"the":[10,35,38,41,99,115,146,151,165,169,186,196,203,207],"side-chain":[11,20,116],"atoms":[12],"interact":[13],"with":[14,70,81,128,213],"each":[15],"other.":[16],"Thus,":[17],"accurate":[18,60],"protein":[19,28,32,96,154,227,231],"packing":[21,150],"(PSCP)":[22],"is":[23],"a":[24,71,106,120,214],"critical":[25],"step":[26],"toward":[27],"prediction":[30],"design.":[33],"Despite":[34],"importance":[36],"of":[37,45,77,113,124,199,206,222],"problem,":[39],"however,":[40],"accuracy":[42],"speed":[44,148],"current":[46],"PSCP":[47,61,84],"programs":[48],"still":[50],"not":[51],"satisfactory.":[52],"RESULTS:":[53],"We":[54],"present":[55],"FASPR":[56,78,104,144,174,200,221],"for":[57,149,225],"fast":[58],"using":[63,119],"an":[64,176],"optimized":[65,216],"scoring":[66,217],"in":[68,156,202],"combination":[69,205],"deterministic":[72],"searching":[73],"algorithm.":[74],"The":[75,237],"performance":[76,108,180],"was":[79,161],"compared":[80,126],"four":[82],"state-of-the-art":[83],"methods":[85],"(CISRR,":[86],"RASP,":[87],"SCATD":[88,133],"SCWRL4)":[90],"on":[91,101,171,181],"both":[92,226],"native":[93,102],"non-native":[95,172],"backbones.":[97],"For":[98,168],"assessment":[100,170],"backbones,":[103,173],"achieved":[105,145],"good":[107],"correctly":[110],"predicting":[111],"69.1%":[112],"all":[114],"dihedral":[117],"angles":[118],"stringent":[121],"tolerance":[122],"criterion":[123],"20\u00b0,":[125],"favorably":[127],"SCWRL4,":[129],"CISRR,":[130],"RASP":[131],"which":[134,160,219],"successfully":[135],"predicted":[136,183],"68.8%,":[137],"68.6%,":[138],"67.8%":[139],"61.7%,":[141],"respectively.":[142],"Additionally,":[143],"highest":[147],"379":[152],"test":[153],"structures":[155],"only":[157],"34.3":[158],"s,":[159],"significantly":[162],"faster":[163],"than":[164],"control":[166],"methods.":[167],"showed":[175,194],"equivalent":[177],"or":[178],"better":[179],"I-TASSER":[182],"backbones":[184,187],"perturbed":[188],"from":[189],"experimental":[190],"structures.":[191],"Detailed":[192],"analyses":[193],"that":[195],"major":[197],"advantage":[198],"lies":[201],"optimal":[204],"dead-end":[208],"elimination":[209],"tree":[211],"decomposition":[212],"well":[215],"function,":[218],"makes":[220],"practical":[223],"use":[224],"modeling":[229],"design":[232],"studies.":[233],"AVAILABILITY":[234],"AND":[235],"IMPLEMENTATION:":[236],"web":[238],"server,":[239],"source":[240],"code":[241],"datasets":[243],"freely":[245],"available":[246,256],"at":[247,257],"https://zhanglab.ccmb.med.umich.edu/FASPR":[248],"https://github.com/tommyhuangthu/FASPR.":[250],"SUPPLEMENTARY":[251],"INFORMATION:":[252],"Supplementary":[253],"data":[254],"Bioinformatics":[258],"online.":[259]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":26},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":6},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
