{"id":"https://openalex.org/W2096328857","doi":"https://doi.org/10.1155/2012/849830","title":"CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures","display_name":"CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures","publication_year":2012,"publication_date":"2012-10-10","ids":{"openalex":"https://openalex.org/W2096328857","doi":"https://doi.org/10.1155/2012/849830","mag":"2096328857","pmid":"https://pubmed.ncbi.nlm.nih.gov/23091487"},"language":"en","primary_location":{"id":"doi:10.1155/2012/849830","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/849830","pdf_url":"https://downloads.hindawi.com/journals/abi/2012/849830.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/journals/abi/2012/849830.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021665118","display_name":"Hamed Bostan","orcid":"https://orcid.org/0000-0003-4102-807X"},"institutions":[{"id":"https://openalex.org/I4576418","display_name":"University of Technology Malaysia","ror":"https://ror.org/026w31v75","country_code":"MY","type":"education","lineage":["https://openalex.org/I4576418"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Hamed Bostan","raw_affiliation_strings":["Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia"],"raw_orcid":"https://orcid.org/0000-0003-4102-807X","affiliations":[{"raw_affiliation_string":"Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia","institution_ids":["https://openalex.org/I4576418"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012641332","display_name":"Naomie Salim","orcid":"https://orcid.org/0000-0001-8509-3055"},"institutions":[{"id":"https://openalex.org/I4576418","display_name":"University of Technology Malaysia","ror":"https://ror.org/026w31v75","country_code":"MY","type":"education","lineage":["https://openalex.org/I4576418"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Naomie Salim","raw_affiliation_strings":["Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia","institution_ids":["https://openalex.org/I4576418"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zeti Azura Hussein","orcid":null},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Zeti Azura Hussein","raw_affiliation_strings":["School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053691506","display_name":"Peter Klappa","orcid":null},"institutions":[{"id":"https://openalex.org/I20581793","display_name":"University of Kent","ror":"https://ror.org/00xkeyj56","country_code":"GB","type":"education","lineage":["https://openalex.org/I20581793"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Klappa","raw_affiliation_strings":["School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK","institution_ids":["https://openalex.org/I20581793"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070607734","display_name":"Mohd Shahir Shamsir","orcid":"https://orcid.org/0000-0002-1191-1294"},"institutions":[{"id":"https://openalex.org/I4576418","display_name":"University of Technology Malaysia","ror":"https://ror.org/026w31v75","country_code":"MY","type":"education","lineage":["https://openalex.org/I4576418"]}],"countries":["MY"],"is_corresponding":true,"raw_author_name":"Mohd Shahir Shamsir","raw_affiliation_strings":["Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia"],"raw_orcid":"https://orcid.org/0000-0002-1191-1294","affiliations":[{"raw_affiliation_string":"Faculty of Biosciences and Bioengineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia","institution_ids":["https://openalex.org/I4576418"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5070607734"],"corresponding_institution_ids":["https://openalex.org/I4576418"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.11209949,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"2012","issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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":0.9983999729156494,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9983999729156494,"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":0.9979000091552734,"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/uniprot","display_name":"UniProt","score":0.8569734692573547},{"id":"https://openalex.org/keywords/cysteine","display_name":"Cysteine","score":0.6750612258911133},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6039760708808899},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6028427481651306},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5364454984664917},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5085927248001099},{"id":"https://openalex.org/keywords/structural-motif","display_name":"Structural motif","score":0.4555453360080719},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.4359404444694519},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.42219170928001404},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4132160544395447},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4022148549556732},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3331795930862427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21728432178497314},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1782906949520111},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1582387387752533},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08420222997665405}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.8569734692573547},{"id":"https://openalex.org/C2779201268","wikidata":"https://www.wikidata.org/wiki/Q186474","display_name":"Cysteine","level":3,"score":0.6750612258911133},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6039760708808899},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6028427481651306},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5364454984664917},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5085927248001099},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.4555453360080719},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.4359404444694519},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.42219170928001404},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4132160544395447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4022148549556732},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3331795930862427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21728432178497314},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1782906949520111},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1582387387752533},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08420222997665405},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1155/2012/849830","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/849830","pdf_url":"https://downloads.hindawi.com/journals/abi/2012/849830.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23091487","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23091487","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":"Advances in bioinformatics","raw_type":null},{"id":"pmh:oai:kar.kent.ac.uk:64928","is_oa":false,"landing_page_url":"https://doi.org/10.1155/2012%2F849830>)","pdf_url":null,"source":{"id":"https://openalex.org/S4377196264","display_name":"Kent Academic Repository (University of Kent)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20581793","host_organization_name":"University of Kent","host_organization_lineage":["https://openalex.org/I20581793"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2470473","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3474208","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1155/2012/849830","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2012/849830","pdf_url":"https://downloads.hindawi.com/journals/abi/2012/849830.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321784","display_name":"Kementerian Sains, Teknologi dan Inovasi","ror":"https://ror.org/012s3r374"},{"id":"https://openalex.org/F4320321992","display_name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Inova\u00e7\u00e3o","ror":"https://ror.org/050zdnc69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096328857.pdf","grobid_xml":"https://content.openalex.org/works/W2096328857.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1963916236","https://openalex.org/W1984615569","https://openalex.org/W1985616824","https://openalex.org/W2009904974","https://openalex.org/W2019410563","https://openalex.org/W2061565420","https://openalex.org/W2067395459","https://openalex.org/W2069268753","https://openalex.org/W2097150498","https://openalex.org/W2108305262","https://openalex.org/W2120409251","https://openalex.org/W2126817143","https://openalex.org/W2128667006","https://openalex.org/W2159128192","https://openalex.org/W2171781238"],"related_works":["https://openalex.org/W2162388472","https://openalex.org/W2765199194","https://openalex.org/W3132544722","https://openalex.org/W3181892255","https://openalex.org/W4232154957","https://openalex.org/W2103435205","https://openalex.org/W2022209941","https://openalex.org/W4292058683","https://openalex.org/W2164809504","https://openalex.org/W2133328876"],"abstract_inverted_index":{"Computational":[0],"approaches":[1],"to":[2,162],"the":[3,20,26,31,52,59,81,139,155,180,193],"disulphide":[4,34],"bonding":[5,35,113],"state":[6],"and":[7,40,47,75,94,105,109,127,146,185],"its":[8],"connectivity":[9],"pattern":[10],"prediction":[11],"are":[12,124,132,136],"based":[13,137],"on":[14,138],"various":[15],"descriptors.":[16],"One":[17],"descriptor":[18],"is":[19,43,58],"amino":[21],"acid":[22],"sequence":[23,144,194],"motifs":[24,70,91,122,187],"flanking":[25,69,121],"cysteine":[27,66,90,183],"residue":[28],"motifs.":[29],"Despite":[30],"existence":[32],"of":[33,107,111,116,192],"information":[36,178],"in":[37,151],"many":[38],"databases":[39],"applications,":[41],"there":[42],"no":[44],"complete":[45],"reference":[46],"motif":[48,55,195],"query":[49,163],"available":[50],"at":[51],"moment.":[53],"Cysteine":[54],"database":[56,165],"(CMD)":[57],"first":[60],"online":[61],"resource":[62],"that":[63,123,131,158,188],"stores":[64],"all":[65],"residues,":[67,184],"their":[68,72,112,186],"with":[71,98],"secondary":[73,99,147],"structure,":[74],"propensity":[76,102],"values":[77],"assignment":[78],"derived":[79],"from":[80,92],"laboratory":[82],"data.":[83],"We":[84],"extracted":[85],"more":[86],"than":[87],"3":[88],"million":[89],"PDB":[93],"UniProt":[95],"data,":[96],"annotated":[97],"structure":[100,148],"assignment,":[101,104],"value":[103],"frequency":[106],"occurrence":[108],"coefficiency":[110],"status.":[114],"Removal":[115],"redundancies":[117],"generated":[118],"15875":[119],"unique":[120,129],"always":[125,133],"bonded":[126],"41577":[128],"patterns":[130],"nonbonded.":[134],"Queries":[135],"protein":[140],"ID,":[141],"FASTA":[142],"sequence,":[143],"motif,":[145],"individually":[149],"or":[150],"batch":[152],"format":[153],"using":[154],"provided":[156],"APIs":[157],"allow":[159],"remote":[160],"users":[161],"our":[164],"via":[166],"third":[167],"party":[168],"software":[169],"and/or":[170],"high":[171],"throughput":[172],"screening/querying.":[173],"The":[174],"CMD":[175],"offers":[176],"extensive":[177],"about":[179],"bonded,":[181],"free":[182],"allows":[189],"in-depth":[190],"characterization":[191],"composition.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
