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In this respect, identification of conserved sequence can facilitate understanding and classifying the exact role of proteins. However, the exact role of these conserved elements cannot be elucidated without structural and physiochemical information. In this work, we present a novel desktop application MotViz designed for searching and analyzing the conserved sequence segments within protein structure. With MotViz, the user can extract a complete list of sequence motifs from loaded 3D structures, annotate the motifs structurally and analyze their physiochemical properties. The conservation value calculated for an individual motif can be visualized graphically. To check the efficiency, predicted motifs from the data sets of 9 protein families were analyzed and MotViz algorithm was more efficient in comparison to other online motif prediction tools. Furthermore, a database was also integrated for storing, retrieving and performing the detailed functional annotation studies. In summary, MotViz effectively predicts motifs with high sensitivity and simultaneously visualizes them into 3D strucures. Moreover, MotViz is user-friendly with optimized graphical parameters and better processing speed due to the inclusion of a database at the back end. MotViz is available at http:\/\/www.fi-pk.com\/motviz.html.<\/jats:p>","DOI":"10.1016\/s1672-0229(11)60031-4","type":"journal-article","created":{"date-parts":[[2012,3,23]],"date-time":"2012-03-23T19:31:21Z","timestamp":1332531081000},"page":"35-43","source":"Crossref","is-referenced-by-count":1,"title":["<i>MotViz<\/i>: A Tool for Sequence Motif Prediction in Parallel to Structural Visualization and Analyses"],"prefix":"10.1093","volume":"10","author":[{"given":"Muhammad Sulaman","family":"Nawaz","sequence":"first","affiliation":[{"name":"National Center for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"}]},{"given":"Sajid","family":"Rashid","sequence":"additional","affiliation":[{"name":"National Center for Bioinformatics, Quaid-i-Azam University , Islamabad, 44000 , Pakistan"}]}],"member":"286","published-online":{"date-parts":[[2012,3,23]]},"reference":[{"key":"2024051008293567700_bib1","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051008293567700_bib2","doi-asserted-by":"crossref","first-page":"D392","DOI":"10.1093\/nar\/gkq1021","article-title":"The RCSB Protein Data Bank: redesigned web site and web services","volume":"39","author":"Rose","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2024051008293567700_bib3","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1002\/prot.22458","article-title":"Structure is three to ten times more conserved than sequence--a study of structural response in protein cores","volume":"77","author":"Illergard","year":"2009","journal-title":"Proteins"},{"key":"2024051008293567700_bib4","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/S0968-0004(00)89080-5","article-title":"RASMOL: biomolecular graphics for all","volume":"20","author":"Sayle","year":"1995","journal-title":"Trends Biochem. 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