{"id":"https://openalex.org/W2589205199","doi":"https://doi.org/10.1093/bioinformatics/btx101","title":"BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank","display_name":"BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank","publication_year":2017,"publication_date":"2017-02-16","ids":{"openalex":"https://openalex.org/W2589205199","doi":"https://doi.org/10.1093/bioinformatics/btx101","mag":"2589205199","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334105"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx101","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014978419","display_name":"Jianjiong Gao","orcid":"https://orcid.org/0000-0002-5739-1781"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianjiong Gao","raw_affiliation_strings":["Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077634829","display_name":"Andreas Prli\u0107","orcid":"https://orcid.org/0000-0001-6346-6391"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Prli\u0107","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037719857","display_name":"Chunxiao Bi","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunxiao Bi","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053815083","display_name":"Wolfgang F. Bluhm","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wolfgang F Bluhm","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074348793","display_name":"Dimitris Dimitropoulos","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dimitris Dimitropoulos","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip E Bourne","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070583038","display_name":"Peter W. Rose","orcid":"https://orcid.org/0000-0001-9981-9750"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter W Rose","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5070583038"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.897,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.72823478,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"13","first_page":"2047","last_page":"2049"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.36970001459121704,"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":0.36970001459121704,"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":0.3375999927520752,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0348999984562397,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.9829592704772949},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.924458384513855},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.816072940826416},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5627378821372986},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44194135069847107},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4151042103767395},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3279942572116852},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3213231563568115},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.260169118642807},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10925853252410889},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08939915895462036}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.9829592704772949},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.924458384513855},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.816072940826416},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5627378821372986},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44194135069847107},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4151042103767395},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3279942572116852},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3213231563568115},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.260169118642807},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10925853252410889},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08939915895462036}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx101","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334105","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:escholarship.org:ark:/13030/qt3594r4hm","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/3594r4hm","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 33, iss 13","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5870676","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870676","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx101","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx101","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2047/25155924/btx101.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1661889616","display_name":null,"funder_award_id":"DBI-1338415","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G2276489800","display_name":"PDB Management by the Research Collaboratory for Structural Bioinformatics","funder_award_id":"0829586","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2285748185","display_name":null,"funder_award_id":"DBI-1338415","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2537093902","display_name":null,"funder_award_id":"1338415","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2654126371","display_name":null,"funder_award_id":"NSF DBI-0829586","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2660623004","display_name":null,"funder_award_id":"R01-GM100701","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3880306168","display_name":"PDB Management by the Research Collaboratory for Structural Bioinformatics","funder_award_id":"1338415","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5104178861","display_name":null,"funder_award_id":"R33-GM078601","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5427449508","display_name":null,"funder_award_id":"R01-GM100701","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5535058654","display_name":null,"funder_award_id":"R33-GM078601 and R01-GM100701","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6178848577","display_name":null,"funder_award_id":"DBI-1338415","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6801256034","display_name":null,"funder_award_id":"DBI-1338415","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7213916153","display_name":null,"funder_award_id":"GM100701","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G738318734","display_name":null,"funder_award_id":"1338415","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G809639315","display_name":null,"funder_award_id":"GM100701","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8734895242","display_name":null,"funder_award_id":"NSF DBI DBI-1338415","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/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2589205199.pdf","grobid_xml":"https://content.openalex.org/works/W2589205199.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1975681329","https://openalex.org/W1989962769","https://openalex.org/W1999615477","https://openalex.org/W2021177388","https://openalex.org/W2105803236","https://openalex.org/W2130479394","https://openalex.org/W2157122545","https://openalex.org/W2170441710"],"related_works":["https://openalex.org/W2589205199","https://openalex.org/W2952811294","https://openalex.org/W3126783617","https://openalex.org/W2732388178","https://openalex.org/W3093468851","https://openalex.org/W4353055924","https://openalex.org/W2806488847","https://openalex.org/W2121688928","https://openalex.org/W2134815007","https://openalex.org/W2772651271"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1,43,56,70],"developed":[2,58],"a":[3,59],"new":[4],"software":[5],"tool,":[6],"BioJava-ModFinder,":[7,102],"for":[8],"identifying":[9],"protein":[10,30,68,83,111],"modifications":[11,31,46,65],"observed":[12],"in":[13,17,38,66,98],"3D":[14,67,96],"structures":[15,97,109],"archived":[16],"the":[18,76,87,99,121],"Protein":[19],"Data":[20],"Bank":[21],"(PDB).":[22],"Information":[23],"on":[24,120],"more":[25,105],"than":[26,106],"400":[27],"types":[28],"of":[29],"were":[32],"collected":[33],"and":[34,41,54,81,90,118],"curated":[35],"from":[36],"annotations":[37,85],"PDB,":[39],"RESID,":[40],"PSI-MOD.":[42],"divided":[44],"these":[45,64],"into":[47],"three":[48],"categories:":[49],"modified":[50],"residues,":[51],"attachment":[52],"modifications,":[53,112],"cross-links.":[55],"have":[57,71],"systematic":[60],"method":[61],"to":[62,86],"identify":[63],"structures.":[69],"integrated":[72],"this":[73],"package":[74],"with":[75,110],"RCSB":[77,122,141],"PDB":[78,100,123,142],"web":[79],"application":[80],"added":[82],"modification":[84],"sequence":[88],"diagram":[89],"structure":[91],"display.":[92],"By":[93],"scanning":[94],"all":[95],"using":[101],"we":[103],"identified":[104],"30":[107],"000":[108],"which":[113],"can":[114,143],"be":[115,144],"searched,":[116],"browsed,":[117],"visualized":[119],"website.":[124],"AVAILABILITY":[125],"AND":[126],"IMPLEMENTATION:":[127],"BioJava-ModFinder":[128],"is":[129],"available":[130],"as":[131],"open":[132],"source":[133],"(LGPL":[134],"license)":[135],"at":[136,146],"(":[137],"https://github.com/biojava/biojava/tree/master/biojava-modfinder":[138],").":[139],"The":[140],"accessed":[145],"http://www.rcsb.org":[147],".":[148],"CONTACT:":[149],"pwrose@ucsd.edu.":[150]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
