{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:14:30Z","timestamp":1761059670564},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization.<\/jats:p>\n               <jats:p>Results: We have created the AMASS database, which maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface. Our platform also provides an analysis service that screens mass spectrometry sequence data for post-translational modifications that reside in functionally relevant locations within protein structures. The system is built on the premise that functional residues such as active sites, cancer mutations and post-translational modifications within proteins may co-localize and share common functions.<\/jats:p>\n               <jats:p>Availability and implementation: AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org.<\/jats:p>\n               <jats:p>Contact: \u00a0clinton.mielke@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu073","type":"journal-article","created":{"date-parts":[[2014,2,5]],"date-time":"2014-02-05T01:26:48Z","timestamp":1391563608000},"page":"1595-1600","source":"Crossref","is-referenced-by-count":5,"title":["AMASS: a database for investigating protein structures"],"prefix":"10.1093","volume":"30","author":[{"given":"Clinton J.","family":"Mielke","sequence":"first","affiliation":[{"name":"1 Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, 2The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and 3Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"},{"name":"1 Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, 2The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and 3Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"},{"name":"1 Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, 2The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and 3Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}]},{"given":"Lawrence J.","family":"Mandarino","sequence":"additional","affiliation":[{"name":"1 Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, 2The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and 3Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}]},{"given":"Valentin","family":"Dinu","sequence":"additional","affiliation":[{"name":"1 Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, 2The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and 3Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,2,3]]},"reference":[{"key":"2023012710545085700_btu073-B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471142905.hg0720s76","article-title":"Predicting functional effect of human missense mutations using PolyPhen-2","author":"Adzhubei","year":"2013","journal-title":"Curr. Protoc. Hum. Genet."},{"key":"2023012710545085700_btu073-B3","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B4","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","article-title":"ProDy: protein dynamics inferred from theory and experiments","volume":"27","author":"Bakan","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012710545085700_btu073-B5","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.cell.2012.05.036","article-title":"Systematic functional prioritization of protein posttranslational modifications","volume":"150","author":"Beltrao","year":"2012","journal-title":"Cell"},{"key":"2023012710545085700_btu073-B6","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/0003-9861(78)90204-7","article-title":"The Protein Data Bank: a computer-based archival file for macromolecular structures","volume":"185","author":"Bernstein","year":"1978","journal-title":"Arch. Biochem. Biophys."},{"key":"2023012710545085700_btu073-B7","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.str.2007.12.002","article-title":"Contributions to the NIH-NIGMS protein structure initiative from the PSI production centers","volume":"16","author":"Burley","year":"2008","journal-title":"Structure"},{"key":"2023012710545085700_btu073-B8","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/scientificamerican0307-50","article-title":"Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies","volume":"296","author":"Collins","year":"2007","journal-title":"Sci. Am."},{"key":"2023012710545085700_btu073-B9","doi-asserted-by":"crossref","first-page":"D935","DOI":"10.1093\/nar\/gkr996","article-title":"SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants","volume":"40","author":"De Baets","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B10","doi-asserted-by":"crossref","first-page":"D240","DOI":"10.1093\/nar\/gkm772","article-title":"Phospho.ELM: a database of phosphorylation sites\u2013update 2008","volume":"36","author":"Diella","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B11","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B12","doi-asserted-by":"crossref","first-page":"10436","DOI":"10.1074\/jbc.M212881200","article-title":"Proteome analysis reveals phosphorylation of ATP synthase beta -subunit in human skeletal muscle and proteins with potential roles in type 2 diabetes","volume":"278","author":"Hojlund","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2023012710545085700_btu073-B13","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gkr1122","article-title":"PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse","volume":"40","author":"Hornbeck","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B14","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1016\/j.str.2008.10.010","article-title":"Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops","volume":"16","author":"Kato","year":"2008","journal-title":"Structure"},{"key":"2023012710545085700_btu073-B15","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1016\/j.jprot.2009.06.011","article-title":"Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS\/MS","volume":"72","author":"Lefort","year":"2009","journal-title":"J. Proteomics"},{"key":"2023012710545085700_btu073-B16","doi-asserted-by":"crossref","first-page":"bas018","DOI":"10.1093\/database\/bas018","article-title":"MSV3d: database of human MisSense variants mapped to 3D protein structure","volume":"2012","author":"Luu","year":"2012","journal-title":"Database (Oxford)"},{"key":"2023012710545085700_btu073-B17","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1093\/bioinformatics\/btg241","article-title":"MutDB: annotating human variation with functionally relevant data","volume":"19","author":"Mooney","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012710545085700_btu073-B18","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2023012710545085700_btu073-B19","doi-asserted-by":"crossref","first-page":"D71","DOI":"10.1093\/nar\/gkr981","article-title":"Reorganizing the protein space at the Universal Protein Resource (UniProt)","volume":"40","author":"UniProt","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B20","doi-asserted-by":"crossref","first-page":"D483","DOI":"10.1093\/nar\/gks1258","article-title":"SIFTS: structure integration with function, taxonomy and sequences resource","volume":"41","author":"Velankar","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012710545085700_btu073-B21","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2105-7-166","article-title":"SNPs3D: candidate gene and SNP selection for association studies","volume":"7","author":"Yue","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012710545085700_btu073-B22","doi-asserted-by":"crossref","first-page":"D229","DOI":"10.1093\/nar\/gkl922","article-title":"Phospho3D: a database of three-dimensional structures of protein phosphorylation sites","volume":"35","author":"Zanzoni","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/11\/1595\/48928110\/bioinformatics_30_11_1595.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/11\/1595\/48928110\/bioinformatics_30_11_1595.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:37:49Z","timestamp":1674819469000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/11\/1595\/283143"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,2,3]]},"references-count":21,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2014,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu073","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,6,1]]},"published":{"date-parts":[[2014,2,3]]}}}