Abstract
To investigate the functional sites on a protein and the prediction of binding sites (residues)in proteins, it is often required to identify the binding site residues at different distance threshold from protein three dimensional (3D)structures. For the study of a particular protein chain and its interaction with the ligand in complex form, researchers have to parse the output of different available tools or databases for finding binding-site residues. Here we have developed a tool for calculating amino acid contact distances in proteins at different distance threshold from the 3D-structure of the protein. For an input of protein 3D-structure, ContPro can quickly find all binding-site residues in the protein by calculating distances and also allows researchers to select the different distance threshold, protein chain and ligand of interest. Additionally, it can also parse the protein model (in case of multi model protein coordinate file)and the sequence of selected protein chain in Fasta format from the input 3D-structure. The developed tool will be useful for the identification and analysis of binding sites of proteins from 3D-structure at different distance thresholds. IT CAN BE ACCESSED AT: http://procarb.org/contpro/
Highlights
The function of proteins depends on their interaction with other molecules like proteins, DNA, RNA, carbohydrates and other ligands [1]
In order to understand the mechanism of these interactions it is important to calculate the amino acid contacts at different distance thresholds [2,3,4]
With the help of ContPro (Figure 1), user can identify a binding residue by selecting a protein chain and ligand of interest and retrieve the results in the form of different output files
Summary
The function of proteins depends on their interaction with other molecules like proteins, DNA, RNA, carbohydrates and other ligands [1]. In order to understand the mechanism of these interactions it is important to calculate the amino acid contacts at different distance thresholds [2,3,4]. Binding site residues of proteins can be identified from pictorial databases [6], visualization tools like Ligplot [7], or many other web servers developed earlier [1, 5], but this becomes overwhelmingly imposing when a large set of proteins have to be analyzed.
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