{"id":"https://openalex.org/W2140967213","doi":"https://doi.org/10.1093/bioinformatics/btg035","title":"MINRMS: an efficient algorithm for determining protein structuresimilarity using root-mean-squared-distance","display_name":"MINRMS: an efficient algorithm for determining protein structuresimilarity using root-mean-squared-distance","publication_year":2003,"publication_date":"2003-03-21","ids":{"openalex":"https://openalex.org/W2140967213","doi":"https://doi.org/10.1093/bioinformatics/btg035","mag":"2140967213","pmid":"https://pubmed.ncbi.nlm.nih.gov/12651721"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg035","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg035","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103258932","display_name":"Andrew I. Jewett","orcid":"https://orcid.org/0000-0002-6252-9888"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrew I. Jewett","raw_affiliation_strings":["Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]},{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111598904","display_name":"Conrad C. Huang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Conrad C. Huang","raw_affiliation_strings":["Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]},{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086093811","display_name":"Thomas E. Ferrin","orcid":"https://orcid.org/0000-0001-6227-0637"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas E. Ferrin","raw_affiliation_strings":["Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]},{"raw_affiliation_string":"Computer Graphics Laboratory, Department of Pharmaceutical#N#Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5963,"has_fulltext":false,"cited_by_count":53,"citation_normalized_percentile":{"value":0.82653344,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"5","first_page":"625","last_page":"634"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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":0.9957000017166138,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9937999844551086,"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/algorithm","display_name":"Algorithm","score":0.6307699680328369},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5895790457725525},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5214059352874756},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.49120277166366577},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.46565017104148865},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4565510153770447},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.45361849665641785},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.45328807830810547},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.43445590138435364},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.39199402928352356},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22628051042556763},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12718626856803894},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08757510781288147}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6307699680328369},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5895790457725525},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5214059352874756},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.49120277166366577},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.46565017104148865},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4565510153770447},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.45361849665641785},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.45328807830810547},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.43445590138435364},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.39199402928352356},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22628051042556763},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12718626856803894},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08757510781288147},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009113","descriptor_name":"Muramidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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},{"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/btg035","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg035","pdf_url":null,"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:12651721","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12651721","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2054564944","display_name":null,"funder_award_id":"P41-RR01081","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1512364096","https://openalex.org/W1969404979","https://openalex.org/W1969850472","https://openalex.org/W1977618577","https://openalex.org/W1979147581","https://openalex.org/W2005049999","https://openalex.org/W2012744602","https://openalex.org/W2014160633","https://openalex.org/W2022058405","https://openalex.org/W2026046929","https://openalex.org/W2033783923","https://openalex.org/W2037406737","https://openalex.org/W2050537942","https://openalex.org/W2053281575","https://openalex.org/W2056807348","https://openalex.org/W2074231493","https://openalex.org/W2081158065","https://openalex.org/W2085497102","https://openalex.org/W2097471670","https://openalex.org/W2108138353","https://openalex.org/W2115854254","https://openalex.org/W2121879102","https://openalex.org/W2151367789","https://openalex.org/W2152326664"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W4297427155","https://openalex.org/W2088487249","https://openalex.org/W2111937814","https://openalex.org/W2051969447","https://openalex.org/W1985408726","https://openalex.org/W2061567716","https://openalex.org/W2130940308","https://openalex.org/W2084367350","https://openalex.org/W1981307089"],"abstract_inverted_index":{"MOTIVATION:":[0],"Existing":[1],"algorithms":[2],"for":[3,23,44,49,59,120,139],"automated":[4],"protein":[5,34,112],"structure":[6,35,50],"alignment":[7,26,51,81],"generate":[8],"contradictory":[9],"results":[10],"and":[11,27,56,94,105,134],"are":[12],"difficult":[13],"to":[14,32,88],"interpret.":[15],"An":[16],"algorithm":[17,58,82],"which":[18],"can":[19],"provide":[20],"a":[21,29,42,66,96,140,152],"context":[22],"interpreting":[24],"the":[25,46,69,108,111,137],"uses":[28,83],"simple":[30],"method":[31,117],"characterize":[33],"similarity":[36],"is":[37],"needed.":[38],"RESULTS:":[39],"We":[40],"describe":[41],"heuristic":[43],"limiting":[45],"search":[47,78],"space":[48],"comparisons":[52,121],"between":[53,148],"two":[54,149],"proteins,":[55],"an":[57],"finding":[60],"minimal":[61],"root-mean-squared-distance":[62],"(RMSD)":[63],"alignments":[64],"as":[65],"function":[67],"of":[68,71,85,100,110,122,143],"number":[70],"matching":[72],"residue":[73,93],"pairs":[74],"within":[75],"this":[76],"limited":[77],"space.":[79],"Our":[80],"coordinates":[84],"alpha-carbon":[86],"atoms":[87],"represent":[89],"each":[90],"amino":[91],"acid":[92],"requires":[95],"total":[97],"computation":[98],"time":[99],"O(m(3)":[101],"n(2)),":[102],"where":[103],"m":[104],"n":[106],"denote":[107],"lengths":[109],"sequences.":[113],"This":[114],"makes":[115],"our":[116],"fast":[118],"enough":[119],"moderate-size":[123],"proteins":[124,150],"(fewer":[125],"than":[126],"approximately":[127],"800":[128],"residues)":[129],"on":[130],"current":[131],"workstation-class":[132],"computers":[133],"therefore":[135],"addresses":[136],"need":[138],"systematic":[141],"analysis":[142],"multiple":[144],"plausible":[145],"shape":[146],"similarities":[147],"using":[151],"widely":[153],"accepted":[154],"comparison":[155],"metric.":[156]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
