Authors
Sundaramurthy Pandurangan, Shameer Khader, Raashi Sreenivasan, Sunita Gakkhar, and Sowdhamini Ramanathan
Summary
Folding of a protein from its sequence to its three-dimensional structure is controlled by an ensemble of local and global interactions. Pairwise, triplet and quadruplet residue interactions play a vital role in attaining the stable conformation of the protein structure. As higher order interactions make significant contribution to the potential energy landscape of folded proteins, it is important to identify them to estimate their contributions to the overall stability of a protein structure. In the current era of high-throughput sequencing, due to huge lacunae in the sequence to structure ratio, computational approaches are playing a significant role in understanding the design principles of protein structures. Web servers are currently used as a stable platform for the analysis of protein structures. We have developed a web server HORI : Higher Order Residue Interactions in proteins for the calculation of global and local higher order interaction patterns in protein structures. In this article, we report a detailed bioinformatics protocol to access the HORI Server and to employ this server for the identification of spatial clusters and the calculation of higher order residue interactions in protein structures. HORI Server can be accessed from the URL: http://caps.ncbs.res.in/horiFurther details
The protocol was published on Protocol Exchange on 9 April 2010. To see the entire protocol, click on the source link.Advertisement
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