ArticlePLoS computational biology2014
Use of long term molecular dynamics simulation in predicting cancer associated SNPs.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed.
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- Expanding the genotypic and phenotypic spectrum of EAST/SeSAME syndrome: identification of a novel homozygous mutation (c.194 G > A) in KCNJ10 gene.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2025Article
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- Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1.Briefings in bioinformatics · 2024Article
- Machine Learning Methods for Small Data Challenges in Molecular Science.Chemical reviews · 2023Review
- Impact of highly deleterious non-synonymous polymorphisms on GRIN2A protein's structure and function.PloS one · 2023Article
- A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis.Scientific reports · 2022Article
- Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations.BMC immunology · 2022Article
- Identification, analysis of deleterious SNPs of the human GSR gene and their effects on the structure and functions of associated proteins and other diseases.Scientific reports · 2022Article
- High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Inhibition of Cholesterol Biosynthesis.BioMed research international · 2022Article
- Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning.Informatics in medicine unlocked · 2022Article
- In silico comprehensive analysis of coding and non-coding SNPs in human mTOR protein.PloS one · 2022Article
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- A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy.Scientific reports · 2021Article
- Integrative Bioinformatics approaches to therapeutic gene target selection in various cancers for Nitroglycerin.Scientific reports · 2021Article
- Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays.Scientific reports · 2021Article
- Oncological Ligand-Target Binding Systems and Developmental Approaches for Cancer Theranostics.Molecular biotechnology · 2021Review
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Computational prediction of cancer associated SNPs from the large pool of SNP dataset is now being used as a tool for detecting the probable oncogenes, which are further examined in the wet lab experiments. The lack in prediction accuracy has been a major hurdle in relying on the computational results obtained by implementing multiple tools, platforms and algorithms for cancer associated SNP prediction. Our result obtained from the initial computational compilations suggests the strong chance of Aurora-A G325W mutation (rs11539196) to cause hepatocellular carcinoma. The implementation of molecular dynamics simulation (MDS) approaches has significantly aided in raising the prediction accuracy of these results, but measuring the difference in the convergence time of mutant protein structures has been a challenging task while setting the simulation timescale. The convergence time of most of the protein structures may vary from 10 ns to 100 ns or more, depending upon its size. Thus, in this work we have implemented 200 ns of MDS to aid the final results obtained from computational SNP prediction technique. The MDS results have significantly explained the atomic alteration related with the mutant protein and are useful in elaborating the change in structural conformations coupled with the computationally predicted cancer associated mutation. With further advancements in the computational techniques, it will become much easier to predict such mutations with higher accuracy level.
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