{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:40:38Z","timestamp":1761662438314},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation.<\/jats:p><jats:p>Availability: Web interface, downloadable binaries and documentation at<\/jats:p><jats:p>Contact: \u00a0textal@tamu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl584","type":"journal-article","created":{"date-parts":[[2006,12,1]],"date-time":"2006-12-01T01:24:12Z","timestamp":1164936252000},"page":"375-377","source":"Crossref","is-referenced-by-count":3,"title":["Crystallographic protein model-building on the web"],"prefix":"10.1093","volume":"23","author":[{"given":"Kreshna","family":"Gopal","sequence":"first","affiliation":[{"name":"Department of Computer Science, Texas A&M University 1 \u00a0 1 \u00a0 \u00a0 301 H.R. Bright Building, College Station, TX 77843-3112, USA"}]},{"given":"Erik","family":"McKee","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Texas A&M University 1 \u00a0 1 \u00a0 \u00a0 301 H.R. Bright Building, College Station, TX 77843-3112, USA"}]},{"given":"Tod","family":"Romo","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Texas A&M University 2 \u00a0 2 \u00a0 \u00a0 103 Bio-Bio Building, College Station, TX 77843-2128, USA"}]},{"given":"Reetal","family":"Pai","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Texas A&M University 1 \u00a0 1 \u00a0 \u00a0 301 H.R. Bright Building, College Station, TX 77843-3112, USA"}]},{"given":"Jacob","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Texas A&M University 1 \u00a0 1 \u00a0 \u00a0 301 H.R. Bright Building, College Station, TX 77843-3112, USA"}]},{"given":"James","family":"Sacchettini","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Texas A&M University 2 \u00a0 2 \u00a0 \u00a0 103 Bio-Bio Building, College Station, TX 77843-2128, USA"}]},{"given":"Thomas","family":"Ioerger","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Texas A&M University 1 \u00a0 1 \u00a0 \u00a0 301 H.R. Bright Building, College Station, TX 77843-3112, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,11,30]]},"reference":[{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1107\/S0567739471000986","article-title":"A real-space refinement procedure for proteins","volume":"A27","author":"Diamond","year":"1971","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1002\/(SICI)1097-0134(19990901)36:4<526::AID-PROT16>3.0.CO;2-F","article-title":"A database method for automated electron density map interpretation in protein crystallography","volume":"36","author":"Diller","year":"1999","journal-title":"Proteins Struct. Funct. Genet."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1016\/S0076-6879(03)74012-9","article-title":"The TEXTAL system: artificial intelligence techniques for automated protein model building","volume":"374","author":"Ioerger","year":"2003","journal-title":"Methods Enzymol."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1107\/S0108767390010224","article-title":"Improved methods for building models in electron density maps and the location of errors in these models","volume":"A47","author":"Jones","year":"1991","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","first-page":"179","article-title":"Template convolution to enhance or detect structural features in macromolecular electron density maps","volume":"D53","author":"Kleywegt","year":"1997","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","first-page":"125","article-title":"Analysis of three-dimensional protein images","volume":"7","author":"Leherte","year":"1997","journal-title":"J. AI Res., (JAIR)"},{"key":"2023041109380360100_","first-page":"1013","article-title":"A new software routine that automates the fitting of protein x-ray crystallographic electron density maps","volume":"D57","author":"Levitt","year":"2001","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","first-page":"1514","article-title":"FINDMOL: automated identification of macromolecules in electron-density maps","volume":"D61","author":"McKee","year":"2005","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","first-page":"483","article-title":"Automated tracing of electron density maps of proteins","volume":"D59","author":"Oldfield","year":"2003","journal-title":"Acta Crystallogr."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1038\/8263","article-title":"Automated protein model-building combined with iterative structure refinement","volume":"6","author":"Perrakis","year":"1999","journal-title":"Nat. Struct. Biol."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1109\/MIS.2005.114","article-title":"TEXTAL: AI-based structural determination for X-ray protein crystallography","volume":"20","author":"Romo","year":"2005","journal-title":"IEEE Intell. Syst."},{"key":"2023041109380360100_","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2023041109380360100_","first-page":"45","article-title":"Automated side-chain model-building and sequence assignment by template matching","volume":"D59","author":"Terwilliger","year":"2002","journal-title":"Acta Crystallogr."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/3\/375\/49829473\/bioinformatics_23_3_375.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/3\/375\/49829473\/bioinformatics_23_3_375.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T17:08:19Z","timestamp":1707412099000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/3\/375\/235563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,30]]},"references-count":13,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2007,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl584","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,2,1]]},"published":{"date-parts":[[2006,11,30]]}}}