Journal ArticleDOI
Applications of computational algorithm tools to identify functional SNPs
C. George Priya Doss,C. Sudandiradoss,R. Rajasekaran,Parikshit Choudhury,Priyanka Sinha,Pragnya Hota,Udit Prakash Batra,Sethumadhavan Rao +7 more
Reads0
Chats0
TLDR
This work analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and proposed modeled structure for the mutant proteins and compared them with the native protein.Abstract:
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans Understanding the functions of SNPs can greatly help to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols To explore possible relationships between genetic mutation and phenotypic variation, different computational algorithm tools like Sorting Intolerant from Tolerant, Polymorphism Phenotyping, UTRscan, FASTSNP, and PupaSuite were used for prioritization of high-risk SNPs in coding region (exonic nonsynonymous SNPs) and noncoding regions (intronic and exonic 5' and 3'-untranslated region (UTR) SNPs) In this work, we have analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and for providing a guide to experimental work We identified the possible mutations and proposed modeled structure for the mutant proteins and compared them with the native protein These nsSNPs play a critical role in cancer association studies aiming to explain the disparity in cancer treatment responses as well as to improve the effectiveness of the cancer treatments Our results endorse the study with in vivo experimental protocolsread more
Citations
More filters
Journal ArticleDOI
Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective.
TL;DR: This paper represents a computational pipeline in anaplastic lymphoma kinase for SNP-centred study by the application of in silico prediction methods, molecular docking, and molecular dynamics simulation approaches that provides a way in understanding the impact of deleterious mutations in altering the protein drug targets and eventually leading to variable patient's drug response.
Journal ArticleDOI
Computational refinement of functional single nucleotide polymorphisms associated with ATM gene.
C. George Priya Doss,B. Rajith +1 more
TL;DR: This work systematically analyzed and characterized the functional variants in both coding and non coding region that can alter the expression and function of ATM gene and extended the approach on SNPs that could potentially influence protein Post Translational Modifications in ATM gene.
Journal ArticleDOI
Association between Variations in Cell Cycle Genes and Idiopathic Pulmonary Fibrosis
Nicoline M. Korthagen,Coline H.M. van Moorsel,Nicole P. Barlo,Karin M. Kazemier,Henk J.T. Ruven,Jan C. Grutters +5 more
TL;DR: This is the first study to show that genetic variations in the cell cycle genes encoding p53 and p21 are associated with IPF disease development and progression, and support the idea that cell cycle control plays a role in the pathology of IPF.
Journal ArticleDOI
Path to Facilitate the Prediction of Functional Amino Acid Substitutions in Red Blood Cell Disorders – A Computational Approach
B. Rajith,George Priya Doss C +1 more
TL;DR: This study performed a comprehensive analysis of deleterious SNPs at both functional and structural level in the respective genes associated with red blood cell metabolism disorders using bioinformatics tools and identified potential candidate SNPs for future studies in human Red Blood Cell disorders.
Book ChapterDOI
Computational approaches and resources in single amino acid substitutions analysis toward clinical research.
TL;DR: An overview of the existing repositories of variant databases and computational methods in predicting the effects of functional SAPs on protein stability, structure, function, drug response, and protein dynamics is described.
References
More filters
Journal ArticleDOI
p53 mutations in human cancers
TL;DR: The p53 mutational spectrum differs among cancers of the colon, lung, esophagus, breast, liver, brain, reticuloendothelial tissues, and hemopoietic tissues as mentioned in this paper.
Journal ArticleDOI
Surfing the p53 network
TL;DR: The p53 tumour-suppressor gene integrates numerous signals that control cell life and death, and the disruption of p53 has severe consequences when a highly connected node in the Internet breaks down.
Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
Journal ArticleDOI
SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.
Journal ArticleDOI
Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.