{"id":"https://openalex.org/W2329526850","doi":"https://doi.org/10.1093/bioinformatics/btw182","title":"ProtPOS: a python package for the prediction of protein preferred orientation on a surface","display_name":"ProtPOS: a python package for the prediction of protein preferred orientation on a surface","publication_year":2016,"publication_date":"2016-04-10","ids":{"openalex":"https://openalex.org/W2329526850","doi":"https://doi.org/10.1093/bioinformatics/btw182","mag":"2329526850","pmid":"https://pubmed.ncbi.nlm.nih.gov/27153619"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw182","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw182","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2537/49019981/bioinformatics_32_16_2537.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"software-paper","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2537/49019981/bioinformatics_32_16_2537.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029171846","display_name":"Jimmy C. F. Ngai","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jimmy C. F. Ngai","raw_affiliation_strings":["1 Department of Computer and Information Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058845450","display_name":"Pui\u2010In Mak","orcid":"https://orcid.org/0000-0002-3579-8740"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Pui-In Mak","raw_affiliation_strings":["2 State-Key Laboratory of Analog and Mixed-Signal VLSI, Faculty of Science and Technology, University of Macau (UM), Avenida da Universidade, Taipa, Macau, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 State-Key Laboratory of Analog and Mixed-Signal VLSI, Faculty of Science and Technology, University of Macau (UM), Avenida da Universidade, Taipa, Macau, China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102848446","display_name":"Shirley W. I. Siu","orcid":"https://orcid.org/0000-0002-3695-7758"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shirley W. I. Siu","raw_affiliation_strings":["1 Department of Computer and Information Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer and Information Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102848446"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":null,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":"16","first_page":"2537","last_page":"2538"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10859","display_name":"Polymer Surface Interaction Studies","score":0.34209999442100525,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10859","display_name":"Polymer Surface Interaction Studies","score":0.34209999442100525,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"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/T12012","display_name":"Diatoms and Algae Research","score":0.09969999641180038,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.07940000295639038,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9175403714179993},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7050473690032959},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6323994398117065},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5863267183303833},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5774893164634705},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5540857315063477},{"id":"https://openalex.org/keywords/adsorption","display_name":"Adsorption","score":0.5036947131156921},{"id":"https://openalex.org/keywords/surface-protein","display_name":"Surface protein","score":0.41112518310546875},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22090867161750793},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.18729519844055176},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.1702793538570404},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15194952487945557}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9175403714179993},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7050473690032959},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6323994398117065},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5863267183303833},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5774893164634705},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5540857315063477},{"id":"https://openalex.org/C150394285","wikidata":"https://www.wikidata.org/wiki/Q180254","display_name":"Adsorption","level":2,"score":0.5036947131156921},{"id":"https://openalex.org/C3019232848","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Surface protein","level":2,"score":0.41112518310546875},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22090867161750793},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.18729519844055176},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.1702793538570404},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15194952487945557},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw182","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw182","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2537/49019981/bioinformatics_32_16_2537.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27153619","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27153619","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:europepmc.org:3943381","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4978930","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/16/2537","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/16/2537","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw182","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw182","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/16/2537/49019981/bioinformatics_32_16_2537.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G8585463892","display_name":null,"funder_award_id":"MYRG2014-00104-FST","funder_id":"https://openalex.org/F4320322841","funder_display_name":"Universidade de Macau"}],"funders":[{"id":"https://openalex.org/F4320322841","display_name":"Universidade de Macau","ror":"https://ror.org/01r4q9n85"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2329526850.pdf","grobid_xml":"https://content.openalex.org/works/W2329526850.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1976720082","https://openalex.org/W1978161967","https://openalex.org/W1980040861","https://openalex.org/W1987902573","https://openalex.org/W1989274069","https://openalex.org/W2000541359","https://openalex.org/W2028873222","https://openalex.org/W2037411563","https://openalex.org/W2044373798","https://openalex.org/W2061895862","https://openalex.org/W2065237248","https://openalex.org/W2088646498","https://openalex.org/W2334753595"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W1486009489","https://openalex.org/W2995057966","https://openalex.org/W2088034942","https://openalex.org/W4380871953","https://openalex.org/W2149263892","https://openalex.org/W1970803054","https://openalex.org/W2038982061","https://openalex.org/W4251359147"],"abstract_inverted_index":{"UNLABELLED:":[0],"Atomistic":[1],"molecular":[2],"dynamics":[3,14],"simulation":[4,114],"is":[5,21,56,91,120],"a":[6,57,70,76],"promising":[7],"technique":[8],"to":[9,25,95],"investigate":[10],"the":[11,16,31,37,43,46,82,102],"energetics":[12],"and":[13,59,106,125],"in":[15,35],"protein-surface":[17],"adsorption":[18,38],"process":[19],"which":[20,55],"of":[22,33,42,72,85,89],"high":[23],"relevance":[24],"modern":[26],"biotechnological":[27],"applications.":[28],"To":[29],"increase":[30],"chance":[32],"success":[34],"simulating":[36],"process,":[39],"favorable":[40],"orientations":[41,68],"protein":[44,67],"at":[45,104,128,136],"surface":[47,71],"must":[48],"be":[49],"determined.":[50],"Here,":[51],"we":[52],"present":[53],"ProtPOS":[54,90,119],"lightweight":[58],"easy-to-use":[60],"python":[61],"package":[62],"that":[63],"can":[64],"predict":[65],"low-energy":[66],"on":[69],"interest.":[73],"It":[74],"combines":[75],"fast":[77],"conformational":[78],"sampling":[79],"algorithm":[80],"with":[81],"energy":[83],"calculation":[84],"GROMACS.":[86],"The":[87],"advantage":[88],"it":[92],"allows":[93],"users":[94],"select":[96],"any":[97],"force":[98],"fields":[99],"suitable":[100],"for":[101,112,123],"system":[103],"hand":[105],"provide":[107],"structural":[108],"output":[109],"readily":[110],"available":[111,122,135],"further":[113],"studies.":[115],"AVAILABILITY":[116],"AND":[117],"IMPLEMENTATION:":[118],"freely":[121],"academic":[124],"non-profit":[126],"uses":[127],"http://cbbio.cis.umac.mo/software/protpos":[129],"SUPPLEMENTARY":[130],"INFORMATION:":[131],"Supplementary":[132],"data":[133],"are":[134],"Bioinformatics":[137],"online.":[138],"CONTACT:":[139],"shirleysiu@umac.mo.":[140]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
