{"id":"https://openalex.org/W2150705899","doi":"https://doi.org/10.1093/bioinformatics/bti630","title":"MESHI: a new library of Java classes for molecular modeling","display_name":"MESHI: a new library of Java classes for molecular modeling","publication_year":2005,"publication_date":"2005-08-16","ids":{"openalex":"https://openalex.org/W2150705899","doi":"https://doi.org/10.1093/bioinformatics/bti630","mag":"2150705899","pmid":"https://pubmed.ncbi.nlm.nih.gov/16105898"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3931/48981034/bioinformatics_21_20_3931.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3931/48981034/bioinformatics_21_20_3931.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068972788","display_name":"Nir Kalisman","orcid":"https://orcid.org/0000-0003-1615-7136"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"N. Kalisman","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel","Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067392096","display_name":"A. Levi","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"A. Levi","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069291894","display_name":"Tatiana Maximova","orcid":"https://orcid.org/0000-0002-5605-0678"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"T. Maximova","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022779069","display_name":"Dan Reshef","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"D. Reshef","raw_affiliation_strings":["Department of Life Science, Ben-Gurion University Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Science, Ben-Gurion University Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079981809","display_name":"S. Zafriri-Lynn","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"S. Zafriri-Lynn","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107641352","display_name":"Y. Gleyzer","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Y. Gleyzer","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072753313","display_name":"Chen Keasar","orcid":"https://orcid.org/0000-0003-0994-1520"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"C. Keasar","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University, Beer-Sheva 84105, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5056,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.64497343,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"20","first_page":"3931","last_page":"3932"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.21119999885559082,"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":0.21119999885559082,"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":0.16300000250339508,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.1535000056028366,"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/computer-science","display_name":"Computer science","score":0.7260826230049133},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6801483631134033},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5283050537109375},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5199186205863953},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5083557963371277},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5018012523651123},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.454266220331192},{"id":"https://openalex.org/keywords/presentation","display_name":"Presentation (obstetrics)","score":0.4331783652305603},{"id":"https://openalex.org/keywords/object-oriented-programming","display_name":"Object-oriented programming","score":0.42036721110343933},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.40234375}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7260826230049133},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6801483631134033},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5283050537109375},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5199186205863953},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5083557963371277},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5018012523651123},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.454266220331192},{"id":"https://openalex.org/C2777601897","wikidata":"https://www.wikidata.org/wiki/Q3409113","display_name":"Presentation (obstetrics)","level":2,"score":0.4331783652305603},{"id":"https://openalex.org/C73752529","wikidata":"https://www.wikidata.org/wiki/Q79872","display_name":"Object-oriented programming","level":2,"score":0.42036721110343933},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.40234375},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3931/48981034/bioinformatics_21_20_3931.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:16105898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16105898","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/20/3931/48981034/bioinformatics_21_20_3931.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1486913019","https://openalex.org/W1994959402","https://openalex.org/W2013785414","https://openalex.org/W2041189078","https://openalex.org/W2045598937","https://openalex.org/W2051434435","https://openalex.org/W2166711652","https://openalex.org/W2172391442","https://openalex.org/W4254895528"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W2618286804","https://openalex.org/W352609212","https://openalex.org/W2329643025","https://openalex.org/W1511772879","https://openalex.org/W4379115841","https://openalex.org/W2121696621","https://openalex.org/W2109693630","https://openalex.org/W3088304681"],"abstract_inverted_index":{"UNLABELLED:":[0],"Adapting":[1],"a":[2,32,44,94,105],"modular":[3],"and":[4,22,59,64,69,101,103],"object-oriented":[5],"approach":[6],"in":[7,40],"the":[8,16,52,78,113,116],"design":[9],"of":[10,47,55,97,108],"molecular":[11,36,56,58],"modeling":[12,37],"packages":[13,100],"may":[14],"reduce":[15],"software":[17],"development":[18],"barrier":[19],"between":[20],"ideas":[21],"their":[23],"programed":[24],"applications.":[25],"Towards":[26],"this":[27],"goal":[28],"we":[29],"developed":[30],"MESHI,":[31],"new,":[33],"strictly":[34],"object-oriented,":[35],"suite":[38],"written":[39],"Java.":[41],"MESHI":[42,68,79,114],"provides":[43],"comprehensive":[45],"library":[46],"extendable":[48],"classes":[49],"for":[50],"all":[51],"essential":[53],"components":[54],"modeling:":[57],"geometry":[60],"elements,":[61],"energy":[62],"functions":[63],"optimization":[65],"methods.":[66],"AVAILABILITY:":[67],"its":[70],"related":[71],"documentation":[72],"are":[73],"freely":[74],"available":[75,82],"at":[76,83],"http://www.cs.bgu.ac.il/~meshi;":[77],"API":[80],"is":[81],"http://www.cs.bgu.ac.il/~meshi/API":[84],"CONTACT:":[85],"keasar@cs.bgu.ac.il":[86],"SUPPLEMENTARY":[87],"INFORMATION:":[88],"The":[89],"Supplementary":[90],"information":[91],"includes":[92],"(1)":[93],"detailed":[95],"description":[96],"several":[98],"key":[99],"classes,":[102],"(2)":[104],"brief":[106],"presentation":[107],"results":[109],"achieved":[110],"by":[111],"using":[112],"application--Beautify--in":[115],"CASP6":[117],"experiment.":[118]},"counts_by_year":[{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
