{"id":"https://openalex.org/W2892284856","doi":"https://doi.org/10.1093/bioinformatics/bty598","title":"Protein pocket detection via convex hull surface evolution and associated Reeb graph","display_name":"Protein pocket detection via convex hull surface evolution and associated Reeb graph","publication_year":2018,"publication_date":"2018-07-06","ids":{"openalex":"https://openalex.org/W2892284856","doi":"https://doi.org/10.1093/bioinformatics/bty598","mag":"2892284856","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423105"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty598","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i830/25702539/bty598.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/34/17/i830/25702539/bty598.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061659324","display_name":"Rundong Zhao","orcid":"https://orcid.org/0000-0001-6033-4457"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rundong Zhao","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021484581","display_name":"Zixuan Cang","orcid":"https://orcid.org/0000-0002-9951-5586"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zixuan Cang","raw_affiliation_strings":["Department of Mathematics, Michigan State University, East Lansing, MI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042762771","display_name":"Yiying Tong","orcid":"https://orcid.org/0000-0002-7929-4333"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yiying Tong","raw_affiliation_strings":["Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038778212","display_name":"Guo\u2010Wei Wei","orcid":"https://orcid.org/0000-0002-5781-2937"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guo-Wei Wei","raw_affiliation_strings":["Department of Mathematics, Michigan State University, East Lansing, MI, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038778212","https://openalex.org/A5042762771"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2869,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.80235866,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"17","first_page":"i830","last_page":"i837"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9954000115394592,"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/convex-hull","display_name":"Convex hull","score":0.5340473055839539},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5110881924629211},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.48463210463523865},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4808555245399475},{"id":"https://openalex.org/keywords/morse-theory","display_name":"Morse theory","score":0.48083290457725525},{"id":"https://openalex.org/keywords/eikonal-equation","display_name":"Eikonal equation","score":0.4333059787750244},{"id":"https://openalex.org/keywords/differential-geometry","display_name":"Differential geometry","score":0.4195137023925781},{"id":"https://openalex.org/keywords/regular-polygon","display_name":"Regular polygon","score":0.41832882165908813},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32240182161331177},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3201363682746887},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.31803035736083984},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.19116336107254028},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.10963758826255798},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.10016071796417236}],"concepts":[{"id":"https://openalex.org/C206194317","wikidata":"https://www.wikidata.org/wiki/Q1138624","display_name":"Convex hull","level":3,"score":0.5340473055839539},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5110881924629211},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.48463210463523865},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4808555245399475},{"id":"https://openalex.org/C156730297","wikidata":"https://www.wikidata.org/wiki/Q2296951","display_name":"Morse theory","level":2,"score":0.48083290457725525},{"id":"https://openalex.org/C40375134","wikidata":"https://www.wikidata.org/wiki/Q1303846","display_name":"Eikonal equation","level":2,"score":0.4333059787750244},{"id":"https://openalex.org/C192939610","wikidata":"https://www.wikidata.org/wiki/Q188444","display_name":"Differential geometry","level":2,"score":0.4195137023925781},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.41832882165908813},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32240182161331177},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3201363682746887},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.31803035736083984},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.19116336107254028},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.10963758826255798},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.10016071796417236}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty598","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i830/25702539/bty598.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:30423105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423105","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:5675861","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6129271","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty598","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i830/25702539/bty598.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":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G5298411683","display_name":null,"funder_award_id":"1R01GM126189-01A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5822364445","display_name":null,"funder_award_id":"DMS-1721024","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G654540421","display_name":null,"funder_award_id":"CCF- 1655422","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7398210851","display_name":null,"funder_award_id":"DMS-1761320","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2892284856.pdf","grobid_xml":"https://content.openalex.org/works/W2892284856.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1517566065","https://openalex.org/W1973076897","https://openalex.org/W1981254997","https://openalex.org/W1983304433","https://openalex.org/W1990495809","https://openalex.org/W1999244633","https://openalex.org/W2002165972","https://openalex.org/W2004175162","https://openalex.org/W2007624258","https://openalex.org/W2009883354","https://openalex.org/W2015115140","https://openalex.org/W2016936988","https://openalex.org/W2019951137","https://openalex.org/W2025817850","https://openalex.org/W2027130342","https://openalex.org/W2029315739","https://openalex.org/W2031194866","https://openalex.org/W2031973565","https://openalex.org/W2045545335","https://openalex.org/W2049391017","https://openalex.org/W2055061536","https://openalex.org/W2058463742","https://openalex.org/W2072287929","https://openalex.org/W2077776336","https://openalex.org/W2078959398","https://openalex.org/W2092285329","https://openalex.org/W2096736341","https://openalex.org/W2099332139","https://openalex.org/W2101560656","https://openalex.org/W2103794058","https://openalex.org/W2105902442","https://openalex.org/W2112794559","https://openalex.org/W2113167159","https://openalex.org/W2139362074","https://openalex.org/W2140407975","https://openalex.org/W2144044408","https://openalex.org/W2158076215","https://openalex.org/W2164088236","https://openalex.org/W2165565773","https://openalex.org/W2166225722","https://openalex.org/W2331081566","https://openalex.org/W2512253991","https://openalex.org/W2554678109","https://openalex.org/W2569129743","https://openalex.org/W2942900780","https://openalex.org/W2951983287","https://openalex.org/W4212781311","https://openalex.org/W6817498033"],"related_works":["https://openalex.org/W4391016819","https://openalex.org/W2608807293","https://openalex.org/W2911626006","https://openalex.org/W2551432773","https://openalex.org/W2188468195","https://openalex.org/W4321472356","https://openalex.org/W2626226742","https://openalex.org/W2474675250","https://openalex.org/W954578697","https://openalex.org/W1991822465"],"abstract_inverted_index":{"Source":[0],"code":[1],"available":[2,6],"at":[3,7],"https://github.com/rdzhao/ProteinPocketDetection.":[4],"Webserver":[5],"http://weilab.math.msu.edu/PPD/.":[8]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}