{"id":"https://openalex.org/W2130520896","doi":"https://doi.org/10.1093/nar/gkp339","title":"INTREPID: a web server for prediction of functionally important residues by evolutionary analysis","display_name":"INTREPID: a web server for prediction of functionally important residues by evolutionary analysis","publication_year":2009,"publication_date":"2009-05-13","ids":{"openalex":"https://openalex.org/W2130520896","doi":"https://doi.org/10.1093/nar/gkp339","mag":"2130520896","pmid":"https://pubmed.ncbi.nlm.nih.gov/19443452"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkp339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp339","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W390/3930690/gkp339.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":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W390/3930690/gkp339.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049741676","display_name":"Sriram Sankararaman","orcid":"https://orcid.org/0000-0003-1586-9641"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Sankararaman","raw_affiliation_strings":["Department of Computer Science, University of California, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071679223","display_name":"Bryan Kolaczkowski","orcid":"https://orcid.org/0000-0002-9490-6019"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Kolaczkowski","raw_affiliation_strings":["Department of Computer Science, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, USA","Department of Computer Science, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Computer Science, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107849607","display_name":"Kimmen Sj\u00f6lander","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"K. Sjolander","raw_affiliation_strings":["Department of Computer Science, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, USA","Department of Computer Science, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, 2 Department of Bioengineering and 3 Department of Plant and Microbial Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Computer Science, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5107849607"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.4302,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.89062694,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"Web Server","first_page":"W390","last_page":"W395"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9929999709129333,"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/web-server","display_name":"Web server","score":0.8449018001556396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8052815198898315},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.66142737865448},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6222071647644043},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48770245909690857},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.46386685967445374},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45890042185783386},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4235735237598419},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.39078208804130554},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3181774318218231},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2677209973335266},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.25829875469207764},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.25542598962783813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2499902844429016},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10058450698852539}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.8449018001556396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8052815198898315},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.66142737865448},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6222071647644043},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48770245909690857},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.46386685967445374},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45890042185783386},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4235735237598419},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.39078208804130554},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3181774318218231},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2677209973335266},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.25829875469207764},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.25542598962783813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2499902844429016},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10058450698852539},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","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},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkp339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp339","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W390/3930690/gkp339.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":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:19443452","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19443452","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:ark:/13030/qt9hg8r7bh","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.187.8781","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.187.8781","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.berkeley.edu/%7Esriram_s/publications/intrepid-webserver.pdf","raw_type":"text"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt9hg8r7bh","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9hg8r7bh","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic acids research, vol 37, iss Web Server issue","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2703888","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2703888","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/gkp339","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkp339","pdf_url":"https://academic.oup.com/nar/article-pdf/37/suppl_2/W390/3930690/gkp339.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":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.699999988079071}],"awards":[{"id":"https://openalex.org/G3383614831","display_name":null,"funder_award_id":"HG002769","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130520896.pdf"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1561011671","https://openalex.org/W1964640688","https://openalex.org/W1967293793","https://openalex.org/W1982226220","https://openalex.org/W2023385944","https://openalex.org/W2027542060","https://openalex.org/W2043904638","https://openalex.org/W2055033601","https://openalex.org/W2094290815","https://openalex.org/W2106241755","https://openalex.org/W2118488195","https://openalex.org/W2132926880","https://openalex.org/W2149057166","https://openalex.org/W2150444353","https://openalex.org/W2154333184","https://openalex.org/W2162566191","https://openalex.org/W2162574056","https://openalex.org/W2166705366","https://openalex.org/W2168563301","https://openalex.org/W2170471837"],"related_works":["https://openalex.org/W2057191541","https://openalex.org/W2150471837","https://openalex.org/W4242650659","https://openalex.org/W2746882944","https://openalex.org/W2105364679","https://openalex.org/W4290667473","https://openalex.org/W2135668486","https://openalex.org/W1996516710","https://openalex.org/W2108893546","https://openalex.org/W2776264363"],"abstract_inverted_index":{"We":[0],"present":[1],"the":[2,19,63],"INTREPID":[3,13,64,97],"web":[4,43,98],"server":[5,44,99],"for":[6],"predicting":[7],"functionally":[8,77],"important":[9,78],"residues":[10],"in":[11],"proteins.":[12],"has":[14],"been":[15],"shown":[16],"to":[17,35,66,70,75],"boost":[18],"recall":[20],"and":[21,31,57,60],"precision":[22],"of":[23,39,90],"catalytic":[24],"residue":[25],"prediction":[26],"over":[27],"other":[28,37],"sequence-based":[29],"methods":[30],"can":[32],"be":[33,76],"used":[34],"identify":[36],"types":[38],"functional":[40],"residues.":[41],"The":[42,96],"takes":[45],"an":[46],"input":[47],"protein":[48],"sequence,":[49],"gathers":[50],"homologs,":[51],"constructs":[52],"a":[53,68],"multiple":[54],"sequence":[55],"alignment":[56],"phylogenetic":[58],"tree":[59],"finally":[61],"runs":[62],"method":[65],"assign":[67],"score":[69],"each":[71],"position.":[72],"Residues":[73],"predicted":[74],"are":[79],"displayed":[80],"on":[81],"homologous":[82],"3D":[83],"structures":[84],"(where":[85],"available),":[86],"highlighting":[87],"spatial":[88],"patterns":[89],"conservation":[91],"at":[92,102],"various":[93],"significance":[94],"thresholds.":[95],"is":[100],"available":[101],"http://phylogenomics.berkeley.edu/intrepid.":[103]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
