ArticleF1000Research2014
ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex.
Article in F1000Research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Semirational design and engineering of grapevine glucosyltransferases for enhanced activity and modified product selectivity.Glycobiology · 2019Article
- Mutational Analysis of Sigma-1 Receptor's Role in Synaptic Stability.Frontiers in neuroscience · 2019Article
- Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant.Analytica chimica acta · 2018Article
- Design of a heme-binding peptide motif adopting a β-hairpin conformation.The Journal of biological chemistry · 2018Article
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- Novel inhibitors targeting Venezuelan equine encephalitis virus capsid protein identified using In Silico Structure-Based-Drug-Design.Scientific reports · 2017Article
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- mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.Scientific reports · 2016Article
- Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.Journal of computer-aided molecular design · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
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Registered trials
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