CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods

• Published in: Nucleic acids research 2012-07, Vol.40 (Web Server issue), p.W329-W333
• Main Authors: Kozma, Dániel, Simon, István, Tusnády, Gábor E
• Format: Article
• Language: English
• Subjects: Amino Acids - chemistry; Internet; Models, Molecular; Protein Conformation; Sequence Alignment; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks488

A contact map is a 2D derivative of the 3D structure of proteins, containing various residue-residue (RR) contacts within the structure. Contact maps can be used for the reconstruction of structure with high accuracy and can be predicted from the amino acid sequence. Therefore understanding the various properties of contact maps is an important step in protein structure prediction. For investigating basic properties of contact formation and contact clusters we set up an integrated system called Contact Map Web Viewer, or CMWeb for short. The server can be used to visualize contact maps, to link contacts and to show them both in 3D structures and in multiple sequence alignments and to calculate various statistics on contacts. Moreover, we have implemented five contact prediction methods in the CMWeb server to visualize the predicted and real RR contacts in one contact map. The results of other RR contact prediction methods can be uploaded as a benchmark test onto the server as well. All of these functionality is behind a web server, thus for using our application only a Java-capable web browser is needed, no further program installation is required. The CMWeb is freely accessible at http://cmweb.enzim.hu.