{"id":"https://openalex.org/W4402640198","doi":"https://doi.org/10.3389/fcomp.2024.1415648","title":"A lightweight visualization tool for protein unfolding by collision detection and elimination","display_name":"A lightweight visualization tool for protein unfolding by collision detection and elimination","publication_year":2024,"publication_date":"2024-09-19","ids":{"openalex":"https://openalex.org/W4402640198","doi":"https://doi.org/10.3389/fcomp.2024.1415648"},"language":"en","primary_location":{"id":"doi:10.3389/fcomp.2024.1415648","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fcomp.2024.1415648","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/computer-science/articles/10.3389/fcomp.2024.1415648/pdf","source":{"id":"https://openalex.org/S4210211086","display_name":"Frontiers in Computer Science","issn_l":"2624-9898","issn":["2624-9898"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computer Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/computer-science/articles/10.3389/fcomp.2024.1415648/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102081901","display_name":"Hua Qian","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124711","display_name":"Suzhou Art & Design Technology Institute","ror":"https://ror.org/02s83b296","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210124711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Qian","raw_affiliation_strings":["School of Digital Arts, Suzhou Art and Design Technology Institute, Suzhou, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Digital Arts, Suzhou Art and Design Technology Institute, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I4210124711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115591301","display_name":"Yu Chen","orcid":"https://orcid.org/0000-0003-3610-594X"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Chen","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071538499","display_name":"Yelu Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yelu Jiang","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071538499"],"corresponding_institution_ids":["https://openalex.org/I3923682"],"apc_list":{"value":1150,"currency":"USD","value_usd":1150},"apc_paid":{"value":1150,"currency":"USD","value_usd":1150},"fwci":0.211,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56443381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"6","issue":null,"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":0.9994999766349792,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9715999960899353,"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/visualization","display_name":"Visualization","score":0.6949330568313599},{"id":"https://openalex.org/keywords/collision","display_name":"Collision","score":0.5600383281707764},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5109952688217163},{"id":"https://openalex.org/keywords/collision-detection","display_name":"Collision detection","score":0.42828524112701416},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3609878420829773},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.19399353861808777},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.1786963939666748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14459580183029175}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6949330568313599},{"id":"https://openalex.org/C121704057","wikidata":"https://www.wikidata.org/wiki/Q352070","display_name":"Collision","level":2,"score":0.5600383281707764},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5109952688217163},{"id":"https://openalex.org/C199668693","wikidata":"https://www.wikidata.org/wiki/Q1550329","display_name":"Collision detection","level":3,"score":0.42828524112701416},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3609878420829773},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.19399353861808777},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.1786963939666748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14459580183029175}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3389/fcomp.2024.1415648","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fcomp.2024.1415648","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/computer-science/articles/10.3389/fcomp.2024.1415648/pdf","source":{"id":"https://openalex.org/S4210211086","display_name":"Frontiers in Computer Science","issn_l":"2624-9898","issn":["2624-9898"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:177d22e2e13b40e2a2e2ceb1d38ba14f","is_oa":true,"landing_page_url":"https://doaj.org/article/177d22e2e13b40e2a2e2ceb1d38ba14f","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":"Frontiers in Computer Science, Vol 6 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fcomp.2024.1415648","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fcomp.2024.1415648","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/computer-science/articles/10.3389/fcomp.2024.1415648/pdf","source":{"id":"https://openalex.org/S4210211086","display_name":"Frontiers in Computer Science","issn_l":"2624-9898","issn":["2624-9898"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computer Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338247","display_name":"Moonshot Research and Development Program","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402640198.pdf","grobid_xml":"https://content.openalex.org/works/W4402640198.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1491063910","https://openalex.org/W1989186326","https://openalex.org/W2005102720","https://openalex.org/W2006356944","https://openalex.org/W2026821880","https://openalex.org/W2027829873","https://openalex.org/W2040108920","https://openalex.org/W2041025044","https://openalex.org/W2045777307","https://openalex.org/W2048950875","https://openalex.org/W2050957868","https://openalex.org/W2058912578","https://openalex.org/W2059206109","https://openalex.org/W2063616898","https://openalex.org/W2071545816","https://openalex.org/W2078574456","https://openalex.org/W2088510066","https://openalex.org/W2088780328","https://openalex.org/W2093537924","https://openalex.org/W2104951158","https://openalex.org/W2122680286","https://openalex.org/W2129020329","https://openalex.org/W2132629607","https://openalex.org/W2141920771","https://openalex.org/W2171268876","https://openalex.org/W2172039086","https://openalex.org/W2319565192","https://openalex.org/W2335558024","https://openalex.org/W2806111497","https://openalex.org/W2920263002","https://openalex.org/W2949223833","https://openalex.org/W2999044305","https://openalex.org/W3036620924","https://openalex.org/W3048016986","https://openalex.org/W3097522440","https://openalex.org/W3139267667","https://openalex.org/W3186179742","https://openalex.org/W3187251571","https://openalex.org/W3201073812","https://openalex.org/W4255584963","https://openalex.org/W4284667229","https://openalex.org/W4286669150","https://openalex.org/W4300980637","https://openalex.org/W4366520892","https://openalex.org/W4391629229"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3138645172","https://openalex.org/W2148917807","https://openalex.org/W3215492696","https://openalex.org/W2257960210","https://openalex.org/W2028510469","https://openalex.org/W913501818","https://openalex.org/W2021628292","https://openalex.org/W4379525781","https://openalex.org/W1987135480"],"abstract_inverted_index":{"The":[0],"experiments":[1],"involving":[2],"protein":[3,29,60,88,118],"denaturation":[4],"and":[5,35,79,81,95,99,121],"refolding":[6],"serve":[7],"as":[8],"the":[9,13,43],"foundation":[10],"for":[11,59,116],"predicting":[12],"three-dimensional":[14],"spatial":[15],"structures":[16],"of":[17,46,87,104],"proteins":[18],"based":[19],"on":[20],"their":[21,51],"amino":[22],"acid":[23],"sequences.":[24],"Despite":[25],"significant":[26],"progress":[27],"in":[28,41],"structure":[30],"engineering,":[31],"exemplified":[32],"by":[33,71],"AlphaFold2":[34],"OmegaFold,":[36],"there":[37],"remains":[38],"a":[39,56,102],"gap":[40],"understanding":[42],"folding":[44,119],"pathways":[45],"polypeptide":[47,89],"chains":[48],"leading":[49],"to":[50],"final":[52],"structures.":[53],"We":[54],"developed":[55],"lightweight":[57],"tool":[58],"unfolding":[61,91],"visualization":[62],"called":[63],"PUV":[64,73],"whose":[65],"graphics":[66],"design":[67],"is":[68],"mainly":[69],"implemented":[70],"OpenGL.":[72],"leverages":[74],"principles":[75],"from":[76],"molecular":[77],"biology":[78],"physics,":[80],"achieves":[82],"rapid":[83],"visual":[84],"dynamics":[85],"simulation":[86],"chain":[90],"through":[92],"mechanical":[93],"force":[94],"atom-level":[96],"collision":[97],"detection":[98],"elimination.":[100],"After":[101],"series":[103],"experimental":[105],"validations,":[106],"we":[107],"believe":[108],"that":[109],"this":[110],"method":[111],"can":[112],"provide":[113],"essential":[114],"support":[115],"investigating":[117],"mechanisms":[120],"pathways.":[122]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
