{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T19:31:24Z","timestamp":1761939084950,"version":"build-2065373602"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually.<\/jats:p>\n               <jats:p>Availability: PROVAT source code can be downloaded from http:\/\/raven.bioc.cam.ac.uk\/~swanand\/Provat1, which also provides a webserver for its calculation component, documentation and examples.<\/jats:p>\n               <jats:p>Contact: \u00a0swanand@cryst.bioc.cam.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti523","type":"journal-article","created":{"date-parts":[[2005,6,3]],"date-time":"2005-06-03T00:14:22Z","timestamp":1117757662000},"page":"3316-3317","source":"Crossref","is-referenced-by-count":15,"title":["PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes"],"prefix":"10.1093","volume":"21","author":[{"given":"Swanand P.","family":"Gore","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David F.","family":"Burke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom L.","family":"Blundell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,6,2]]},"reference":[{"key":"2023051612004667000_B1","doi-asserted-by":"crossref","unstructured":"Barber, C.B., et al. 1996The quickhull algorithm for convex hulls. ACM Trans. Math. Softw.  \u00a022\n\u00a0469\u2013483","DOI":"10.1145\/235815.235821"},{"key":"2023051612004667000_B2","doi-asserted-by":"crossref","unstructured":"Canutescu, A.A., et al. 2003A graph theory algorithm for protein side-chain prediction. Protein Sci.  \u00a012\n\u00a02001\u20132014","DOI":"10.1110\/ps.03154503"},{"key":"2023051612004667000_B3","unstructured":"DeLano, W. The PyMOL User's Manual \u00a02002, San Carlos,CA, USA  DeLano Scientific"},{"key":"2023051612004667000_B4","doi-asserted-by":"crossref","unstructured":"Dupuis, F., et al. 2005Voro3d: 3d Voronoi tessellations applied to protein structures. Bioinformatics  \u00a021\n\u00a01715\u20131716","DOI":"10.1093\/bioinformatics\/bth365"},{"key":"2023051612004667000_B5","doi-asserted-by":"crossref","unstructured":"Lindahl, E., et al. 2001Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod.  \u00a07\n\u00a0306\u2013317","DOI":"10.1007\/s008940100045"},{"key":"2023051612004667000_B6","doi-asserted-by":"crossref","unstructured":"Poupon, A. 2004Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Op. Struct. Biol.  \u00a014\n\u00a0233\u2013241","DOI":"10.1016\/j.sbi.2004.03.010"},{"key":"2023051612004667000_B7","doi-asserted-by":"crossref","unstructured":"Zimmer, R., Wohler, M., Thiele, R. 1998New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics  \u00a014\n\u00a0295\u2013308","DOI":"10.1093\/bioinformatics\/14.3.295"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/15\/3316\/50340674\/bioinformatics_21_15_3316.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/15\/3316\/50340674\/bioinformatics_21_15_3316.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T12:01:41Z","timestamp":1684238501000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/15\/3316\/195753"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,6,2]]},"references-count":7,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2005,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti523","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2005,8]]},"published":{"date-parts":[[2005,6,2]]}}}