{"id":"https://openalex.org/W2065678493","doi":"https://doi.org/10.1093/nar/gkg587","title":"SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules","display_name":"SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2065678493","doi":"https://doi.org/10.1093/nar/gkg587","mag":"2065678493","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824326"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg587","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3356/9487462/gkg587.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/nar/article-pdf/31/13/3356/9487462/gkg587.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022819506","display_name":"A. Hussain","orcid":"https://orcid.org/0000-0003-2580-7161"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"A. S. Z. Hussain","raw_affiliation_strings":["Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560 012, India","Bioinformatics Centre, Supercomputer Education and Research Centre Indian Institute of Science, Bangalore, 560 012, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560 012, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Bioinformatics Centre, Supercomputer Education and Research Centre Indian Institute of Science, Bangalore, 560 012, India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5022819506"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.2151,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55198336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"31","issue":"13","first_page":"3356","last_page":"3358"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9890999794006348,"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/scripting-language","display_name":"Scripting language","score":0.6737432479858398},{"id":"https://openalex.org/keywords/symmetry","display_name":"Symmetry (geometry)","score":0.6544350385665894},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.5933048725128174},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5893272757530212},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5590323805809021},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.5209268927574158},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4725974202156067},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.43718278408050537},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4337228536605835},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.43299150466918945},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3989558517932892},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.36845141649246216},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.345114529132843},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.26744234561920166},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24199479818344116},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.22322869300842285},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.16738075017929077},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13425320386886597},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11219888925552368},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10003751516342163}],"concepts":[{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6737432479858398},{"id":"https://openalex.org/C2779886137","wikidata":"https://www.wikidata.org/wiki/Q21030012","display_name":"Symmetry (geometry)","level":2,"score":0.6544350385665894},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.5933048725128174},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5893272757530212},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5590323805809021},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.5209268927574158},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4725974202156067},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.43718278408050537},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4337228536605835},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.43299150466918945},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3989558517932892},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.36845141649246216},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.345114529132843},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26744234561920166},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24199479818344116},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.22322869300842285},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.16738075017929077},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13425320386886597},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11219888925552368},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10003751516342163},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":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":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkg587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg587","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3356/9487462/gkg587.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824326","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824326","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:eprints.iisc.ac.in:12291","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196309","display_name":"NOT FOUND REPOSITORY (Indian Institute of Science Bangalore)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59270414","host_organization_name":"Indian Institute of Science Bangalore","host_organization_lineage":["https://openalex.org/I59270414"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.511.274","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.511.274","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/13/3356.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158849","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168993","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168993","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168993","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg587","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg587","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3356/9487462/gkg587.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320717","display_name":"Department of Biotechnology, Ministry of Science and Technology, India","ror":"https://ror.org/03tjsyq23"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065678493.pdf","grobid_xml":"https://content.openalex.org/works/W2065678493.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W85390549","https://openalex.org/W1977845138","https://openalex.org/W2016607365","https://openalex.org/W2026258231","https://openalex.org/W2049521571","https://openalex.org/W2102306820","https://openalex.org/W2117514600","https://openalex.org/W2130479394"],"related_works":["https://openalex.org/W2331989206","https://openalex.org/W2008612003","https://openalex.org/W3173828731","https://openalex.org/W45658120","https://openalex.org/W4205178530","https://openalex.org/W613088223","https://openalex.org/W2739025131","https://openalex.org/W2606876474","https://openalex.org/W1974405519","https://openalex.org/W4287121746"],"abstract_inverted_index":{"SEM,":[0,93],"Symmetry":[1],"Equivalent":[2],"Molecules,":[3],"is":[4,67],"a":[5],"web-based":[6],"graphical":[7],"user":[8],"interface":[9,102],"to":[10,29,53],"generate":[11],"and":[12,19,60,72],"visualize":[13,54],"the":[14,24,27,31,36,41,55,61,78,87,98],"symmetry":[15,37,62],"equivalent":[16,38,63],"molecules":[17,39],"(proteins":[18],"nucleic":[20],"acids).":[21],"In":[22],"addition,":[23],"program":[25,48,66],"allows":[26],"users":[28],"save":[30],"three-dimensional":[32,79],"atomic":[33,58],"coordinates":[34],"of":[35],"in":[40,86],"local":[42],"machine.":[43],"The":[44,91],"widely":[45],"recognized":[46],"graphics":[47],"RasMol":[49],"has":[50,73],"been":[51,74],"deployed":[52],"reference":[56],"(input":[57],"coordinates)":[59],"molecules.":[64],"This":[65],"written":[68],"using":[69,82],"CGI/Perl":[70],"scripts":[71],"interfaced":[75],"with":[76],"all":[77],"structures":[80],"(solved":[81],"X-ray":[83],"crystallography)":[84],"available":[85],"Protein":[88],"Data":[89],"Bank.":[90],"program,":[92],"can":[94],"be":[95],"accessed":[96],"over":[97],"World":[99],"Wide":[100],"Web":[101],"at":[103],"http://dicsoft2.physics.iisc.ernet.in/sem/":[104],"or":[105],"http://144.16.71.11/sem/.":[106]},"counts_by_year":[],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}