{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T14:02:42Z","timestamp":1722693762860},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: SimiCon is a web server designed for an automated identification of equivalent protein\u2013ligand atomic contacts in different conformational models of a complex. The contacts are computed with internal coordinate mechanics (ICM) software with respect to molecular symmetry and the results are shown in the browser as text, tables and interactive 3D graphics. The web server can be executed remotely without a browser to allow users to automate multiple calculations.<\/jats:p>\n               <jats:p>Availability: SimiCon is freely available at http:\/\/abagyan.ucsd.edu\/SimiCon<\/jats:p>\n               <jats:p>Contact: \u00a0rabagyan@ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq504","type":"journal-article","created":{"date-parts":[[2010,9,26]],"date-time":"2010-09-26T00:14:03Z","timestamp":1285460043000},"page":"2784-2785","source":"Crossref","is-referenced-by-count":11,"title":["SimiCon: a web tool for protein\u2013ligand model comparison through calculation of equivalent atomic contacts"],"prefix":"10.1093","volume":"26","author":[{"given":"Manuel","family":"Rueda","sequence":"first","affiliation":[{"name":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vsevolod","family":"Katritch","sequence":"additional","affiliation":[{"name":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eugene","family":"Raush","sequence":"additional","affiliation":[{"name":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruben","family":"Abagyan","sequence":"additional","affiliation":[{"name":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"},{"name":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,9,24]]},"reference":[{"key":"2023012507535275400_B1","first-page":"277","article-title":"Identifying errors in three dimensional protein models","volume-title":"Protein Structure: Determination, Analysis, and Applications for Drug Discovery.","author":"Abagyan","year":"2003"},{"key":"2023012507535275400_B2","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1006\/jmbi.1994.1052","article-title":"Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins","volume":"235","author":"Abagyan","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2023012507535275400_B3","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1006\/jmbi.1997.0994","article-title":"Contact area difference (CAD): a robust measure to evaluate accuracy of protein models","volume":"268","author":"Abagyan","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023012507535275400_B4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012507535275400_B5","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/s10822-007-9166-3","article-title":"How to do an evaluation: pitfalls and traps","volume":"22","author":"Hawkins","year":"2008","journal-title":"J. Comput. Aided Mol. Des."},{"key":"2023012507535275400_B6","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1002\/prot.20497","article-title":"Comparing protein-ligand docking programs is difficult","volume":"60","author":"Cole","year":"2005","journal-title":"Prot. Struct. Funct. Bioinform."},{"key":"2023012507535275400_B7","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1021\/jm030331x","article-title":"Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions","volume":"47","author":"Deng","year":"2004","journal-title":"J. Med. Chem."},{"key":"2023012507535275400_B8","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1002\/prot.10381","article-title":"CAPRI: a critical assessment of PRedicted Interactions","volume":"52","author":"Janin","year":"2003","journal-title":"Proteins"},{"key":"2023012507535275400_B9","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1021\/ci049970m","article-title":"Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations","volume":"44","author":"Kroemer","year":"2004","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"2023012507535275400_B10","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1021\/ci600342e","article-title":"Optimizing fragment and scaffold docking by use of molecular interaction fingerprints","volume":"47","author":"Marcou","year":"2007","journal-title":"J. Chem. Inf. Model."},{"key":"2023012507535275400_B11","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nrd2877","article-title":"Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008","volume":"8","author":"Michino","year":"2009","journal-title":"Nat. Rev. Drug Discov."},{"key":"2023012507535275400_B12","doi-asserted-by":"crossref","first-page":"e7394","DOI":"10.1371\/journal.pone.0007394","article-title":"A new method for publishing three-dimensional content","volume":"4","author":"Raush","year":"2009","journal-title":"PLoS One"},{"key":"2023012507535275400_B13","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1002\/anie.196603851","article-title":"Specification of molecular chirality","volume":"5","author":"Sidney","year":"1966","journal-title":"Angew. Chemie Int. Ed."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/21\/2784\/48851398\/bioinformatics_26_21_2784.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/21\/2784\/48851398\/bioinformatics_26_21_2784.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:54:13Z","timestamp":1674633253000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/21\/2784\/213293"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9,24]]},"references-count":13,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2010,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq504","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,11,1]]},"published":{"date-parts":[[2010,9,24]]}}}