Abstract
Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.
Highlights
Deciphering protein function is one of the most active areas of research in biology involving both experimental and theoretical approaches [1,2]
Our results indicate that JAMMING may be used to identify critical residues for protein function that are either critical for keeping the protein structure and/or for its biological function
In order to allow for JAMMING calculations to be executed at the same time either in multiple machines (JavaParty implementation) or through a web interface (Servlet implementation), the three steps were embedded in independent remote objects or JavaTM’s thread
Summary
Deciphering protein function is one of the most active areas of research in biology involving both experimental and theoretical approaches [1,2]. Identification of the critical residues for protein function constitutes a central area of research [3,4,5]. Identification of critical residues in proteins is important for both protein function modulation (e.g., drug design [6]) and protein classification [4]. To this end, protein sequences constitute the first and most abundant source of data to infer protein function and most computational methods designed to identify critical residues are based on the analysis of protein sequences. A residue critical for a protein structure is as well critical for the protein function. Referring to critical residues for protein function includes both types of residues: residues critical for protein structure and/or residues critical for its biological function (e.g., catalysis, binding)
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