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
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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
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Posted ContentDOI
Identification of novel key biomarkers in Simpson-Golabi-Behmel Syndrome: Evidence from bioinformatics analysis
Mujahed I. Mustafa,Abdelrahman H. Abdelmoneim,Nafisa M. Elfadol,Naseem S. Murshed,Zainab O. Mohammed,Mohamed A. Hassan +5 more
TL;DR: Three novel missense mutations are revealed that are found to be the most deleterious which effect on the GPC3 structure and function.
Posted ContentDOI
Novel mutations within PRSS1 Gene that could potentially cause hereditary pancreatitis: Using Comprehensive in silico Approach
Mujahed I. Mustafa,Abdelrahman H. Abdelmoneim,Nafisa M. Elfadol,Soada Ahmed Osman,Tebyan A. Abdelhameed,Mohamed A. Hassan +5 more
TL;DR: This is the first in silico analysis of structural effect of each SNP in PRSS1 gene using different bioinformatics tools to predict Single-nucleotide polymorphisms influence on protein structure and function.
Journal ArticleDOI
Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach
Malik Siddique Mahmood,Maryam Afzal,Hina Batool,Amara Saif,Tahreem Aqdas,Naeem Mahmood Ashraf,Mahjabeen Saleem +6 more
TL;DR: The 3-dimensional modeling and structural comparison of variants with the native protein reveals significant structural and conformational variations after mutations, suggesting disruption in the function of phospholysine phosphohistidine inorganic pyrophosphate phosphatase.
Book ChapterDOI
Role of von Willebrand Factor--A1 Domain Variants P1266L, H1268D, C1272R, and C1272F in VWD: A Molecular Modeling and Simulation Analysis Approach.
TL;DR: Through molecular dynamic simulation analysis over a period of 100 ns showed that four mutations near N-terminal region bring about a change in structure and function of the native VWD protein.
Dissertation
The Role of Sialic Acid Acetylesterase in the Maintenance of B Cell Self Tolerance
TL;DR: It is found that most catalytically dead, diseaseassociated variants of SIAE are partially misfolded, and coimmunoprecipitation studies indicated that mutant SIAe associates with wildtype SiaE in a multimer and acts in a dominant-interfering manner to decrease activity of the wildtype protein.
References
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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.