ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex

Anand, Praveen ; Nagarajan, Deepesh ; Mukherjee, Sumanta ; Chandra, Nagasuma (2015) ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex F1000Research, 3 . Article ID 214. ISSN 2046-1402

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Official URL: https://f1000research.com/articles/3-214

Related URL: http://dx.doi.org/10.12688/f1000research.5165.2

Abstract

Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations.

Item Type:Article
Source:Copyright of this article belongs to F1000 Research Ltd.
ID Code:112684
Deposited On:18 Apr 2018 11:54
Last Modified:18 Apr 2018 11:54

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