{"id":"https://openalex.org/W1988281953","doi":"https://doi.org/10.1007/s10822-011-9477-2","title":"Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites","display_name":"Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites","publication_year":2011,"publication_date":"2011-10-01","ids":{"openalex":"https://openalex.org/W1988281953","doi":"https://doi.org/10.1007/s10822-011-9477-2","mag":"1988281953","pmid":"https://pubmed.ncbi.nlm.nih.gov/22038416"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-011-9477-2","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9477-2","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5022425747","display_name":"Cheng-Tsung Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Cheng-Tsung Lu","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003 Taiwan, ROC. s988306@mail.yzu.edu.tw","Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003 Taiwan, ROC. s988306@mail.yzu.edu.tw","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029468543","display_name":"Shu-An Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Shu-An Chen","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045801615","display_name":"Neil Arvin Breta\u00f1a","orcid":"https://orcid.org/0000-0003-4743-348X"},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Neil Arvin Breta\u00f1a","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028123424","display_name":"Tzu-Hsiu Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzu-Hsiu Cheng","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045675277","display_name":"Tzong-Yi Lee","orcid":"https://orcid.org/0000-0001-8475-7868"},"institutions":[{"id":"https://openalex.org/I99908691","display_name":"Yuan Ze University","ror":"https://ror.org/01fv1ds98","country_code":"TW","type":"education","lineage":["https://openalex.org/I99908691"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzong-Yi Lee","raw_affiliation_strings":["Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Room 3312, 135 Yuan-Tung Road, Chungli, Taoyuan, 32003, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Yuan Ze University, Chungli, Taoyuan, Taiwan, ROC","institution_ids":["https://openalex.org/I99908691"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022425747"],"corresponding_institution_ids":["https://openalex.org/I99908691"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.063,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.75123261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"10","first_page":"987","last_page":"995"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9947999715805054,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9947999715805054,"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":0.9944999814033508,"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":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/carboxylation","display_name":"Carboxylation","score":0.9576345682144165},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.682630717754364},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5591981410980225},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4720476567745209},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.47006353735923767},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.44234147667884827},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.4327211081981659},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.34511950612068176},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.32748323678970337},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2517163157463074},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.08345729112625122},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07739531993865967}],"concepts":[{"id":"https://openalex.org/C24428623","wikidata":"https://www.wikidata.org/wiki/Q901081","display_name":"Carboxylation","level":3,"score":0.9576345682144165},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.682630717754364},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5591981410980225},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4720476567745209},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.47006353735923767},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.44234147667884827},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.4327211081981659},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.34511950612068176},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.32748323678970337},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2517163157463074},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.08345729112625122},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07739531993865967}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015055","descriptor_name":"1-Carboxyglutamic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015055","descriptor_name":"1-Carboxyglutamic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015055","descriptor_name":"1-Carboxyglutamic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019735","descriptor_name":"Carbon-Carbon Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019735","descriptor_name":"Carbon-Carbon Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019735","descriptor_name":"Carbon-Carbon Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-011-9477-2","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9477-2","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:22038416","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22038416","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":"Journal of computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1010867140","https://openalex.org/W1501857460","https://openalex.org/W1735160523","https://openalex.org/W1965363899","https://openalex.org/W1969287839","https://openalex.org/W1970899710","https://openalex.org/W1977265717","https://openalex.org/W1977927254","https://openalex.org/W1980042544","https://openalex.org/W1987647241","https://openalex.org/W1999212541","https://openalex.org/W2038804119","https://openalex.org/W2039431699","https://openalex.org/W2041877620","https://openalex.org/W2058579856","https://openalex.org/W2064159479","https://openalex.org/W2070937099","https://openalex.org/W2072603644","https://openalex.org/W2074415016","https://openalex.org/W2098376021","https://openalex.org/W2098550853","https://openalex.org/W2098875971","https://openalex.org/W2102621836","https://openalex.org/W2103017472","https://openalex.org/W2110344625","https://openalex.org/W2111705855","https://openalex.org/W2114528551","https://openalex.org/W2121417968","https://openalex.org/W2129137060","https://openalex.org/W2134468274","https://openalex.org/W2137015675","https://openalex.org/W2154139219","https://openalex.org/W2156070536","https://openalex.org/W2158266834","https://openalex.org/W2408058881"],"related_works":["https://openalex.org/W4322620903","https://openalex.org/W4377028868","https://openalex.org/W2073086338","https://openalex.org/W2053028024","https://openalex.org/W2410006896","https://openalex.org/W2411061118","https://openalex.org/W2035266552","https://openalex.org/W2011602722","https://openalex.org/W2087021784","https://openalex.org/W2020644290"],"abstract_inverted_index":null,"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
