{"id":"https://openalex.org/W4411638902","doi":"https://doi.org/10.1093/bib/bbaf297","title":"To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era","display_name":"To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411638902","doi":"https://doi.org/10.1093/bib/bbaf297","pmid":"https://pubmed.ncbi.nlm.nih.gov/40561466"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf297","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf297","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf297/63581437/bbaf297.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/26/3/bbaf297/63581437/bbaf297.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116443764","display_name":"Sriniketh Vangaru","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sriniketh Vangaru","raw_affiliation_strings":["Department of Computer Science, Virginia Tech , 1160 Torgersen Hall, 620 Drillfield Drive, Blacksburg, VA 24061 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech , 1160 Torgersen Hall, 620 Drillfield Drive, Blacksburg, VA 24061 ,","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Department of Computer Science, Virginia Tech , 1160 Torgersen Hall, 620 Drillfield Drive, Blacksburg, VA 24061 ,"],"raw_orcid":"https://orcid.org/0000-0002-9630-0141","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech , 1160 Torgersen Hall, 620 Drillfield Drive, Blacksburg, VA 24061 ,","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11630031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9937999844551086,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9848999977111816,"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/leverage","display_name":"Leverage (statistics)","score":0.744641125202179},{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.6149728894233704},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5634410381317139},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5467589497566223},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4115096628665924},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2805440127849579},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24740013480186462}],"concepts":[{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.744641125202179},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.6149728894233704},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5634410381317139},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5467589497566223},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4115096628665924},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2805440127849579},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24740013480186462},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf297","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf297","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf297/63581437/bbaf297.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40561466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40561466","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12192453","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12192453","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf297","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf297","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf297/63581437/bbaf297.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G3741541039","display_name":null,"funder_award_id":"R35 GM138146","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3891976813","display_name":null,"funder_award_id":"R35GM138146","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7443050175","display_name":null,"funder_award_id":"DBI2208679","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/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411638902.pdf","grobid_xml":"https://content.openalex.org/works/W4411638902.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1969948291","https://openalex.org/W1991053771","https://openalex.org/W2011658408","https://openalex.org/W2014050554","https://openalex.org/W2015403140","https://openalex.org/W2022846228","https://openalex.org/W2035038973","https://openalex.org/W2106648157","https://openalex.org/W2110682117","https://openalex.org/W2117163574","https://openalex.org/W2140673705","https://openalex.org/W2141685906","https://openalex.org/W2145778523","https://openalex.org/W2151581834","https://openalex.org/W2154042308","https://openalex.org/W2160480536","https://openalex.org/W2163118761","https://openalex.org/W2165371996","https://openalex.org/W2168505829","https://openalex.org/W2201713963","https://openalex.org/W2411608355","https://openalex.org/W2523580724","https://openalex.org/W2556222602","https://openalex.org/W2606439133","https://openalex.org/W2793366908","https://openalex.org/W2890416025","https://openalex.org/W2941939543","https://openalex.org/W2967586821","https://openalex.org/W2994942809","https://openalex.org/W3005725996","https://openalex.org/W3014576393","https://openalex.org/W3100075733","https://openalex.org/W3134805435","https://openalex.org/W3177828909","https://openalex.org/W3183682942","https://openalex.org/W3189787391","https://openalex.org/W4220891150","https://openalex.org/W4220933043","https://openalex.org/W4307627635","https://openalex.org/W4310645193","https://openalex.org/W4315927151","https://openalex.org/W4378782828","https://openalex.org/W4379538527","https://openalex.org/W4385409403","https://openalex.org/W4386317415","https://openalex.org/W4388464011","https://openalex.org/W4391291188","https://openalex.org/W4395053034","https://openalex.org/W4396721167","https://openalex.org/W4399021675","https://openalex.org/W4406213027"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699"],"abstract_inverted_index":{"Protein":[0],"side-chain":[1,8],"packing":[2,103],"(PSCP),":[3],"the":[4,19,27,37,65,79,97,104,121,125,156,170,179],"problem":[5],"of":[6,21,64,68,78,82,90,123],"predicting":[7],"conformations":[9],"given":[10],"a":[11,61,87,133,140],"fixed":[12],"backbone":[13,51,134],"structure,":[14],"has":[15],"important":[16],"implications":[17],"in":[18,30,102,114,176,178],"modeling":[20],"structures":[22],"and":[23,46,164,173],"interactions.":[24],"However,":[25],"despite":[26],"groundbreaking":[28],"progress":[29],"protein":[31],"structure":[32],"prediction":[33],"pioneered":[34],"by":[35,131,147],"AlphaFold,":[36],"existing":[38],"PSCP":[39,55,70,98,177],"methods":[40,71,99],"still":[41],"rely":[42],"on":[43,72],"experimental":[44,107],"inputs,":[45,108],"do":[47],"not":[48,161],"leverage":[49],"AlphaFold-predicted":[50],"coordinates":[52],"to":[53,112,144],"enable":[54],"at":[56],"scale.":[57],"Here,":[58],"we":[59],"perform":[60,100],"large-scale":[62],"benchmarking":[63],"predictive":[66],"performance":[67,145],"various":[69],"public":[73],"datasets":[74],"from":[75,129],"multiple":[76],"rounds":[77],"Critical":[80],"Assessment":[81],"Structure":[83],"Prediction":[84],"challenges":[85,175],"using":[86],"diverse":[88],"set":[89],"evaluation":[91],"metrics.":[92],"Empirical":[93],"results":[94],"demonstrate":[95],"that":[96],"well":[101],"side-chains":[105],"with":[106],"but":[109],"they":[110],"fail":[111],"generalize":[113],"repacking":[115],"AlphaFold-generated":[116],"structures.":[117],"We":[118],"additionally":[119],"explore":[120],"effectiveness":[122],"leveraging":[124],"self-assessment":[126],"confidence":[127],"scores":[128],"AlphaFold":[130,157],"implementing":[132],"confidence-aware":[135],"integrative":[136],"approach.":[137],"While":[138],"such":[139],"protocol":[141],"often":[142],"leads":[143],"improvement":[146],"attaining":[148],"modest":[149],"yet":[150],"statistically":[151],"significant":[152],"accuracy":[153],"gains":[154],"over":[155],"baseline,":[158],"it":[159],"does":[160],"yield":[162],"consistent":[163],"pronounced":[165],"improvements.":[166],"Our":[167],"study":[168],"highlights":[169],"recent":[171],"advances":[172],"remaining":[174],"post-AlphaFold":[180],"era.":[181]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}