4.7 Article

Computational screening and analysis of deleterious nsSNPs in human p14ARF (CDKN2A gene) protein using molecular dynamic simulation approach

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Multidisciplinary

In Silico Drug Designing for ala438 Deleted Ribosomal Protein S1 (RpsA) on the Basis of the Active Compound Zr/15

Abdul Wadood et al.

Summary: Pyrazinoic acid-resistant tuberculosis is a severe chronic disorder characterized by bacterial cell survival due to a mutation in the RpsA protein. In this study, inhibitors were identified using a pharmacophore model and virtual screening, with promising compounds showing potential as antagonists for the mutant state of the RpsA protein.

ACS OMEGA (2022)

Article Chemistry, Multidisciplinary

In Silico Drug Designing for ala438 Deleted Ribosomal Protein S1 (RpsA) on the Basis of the Active Compound Zrl15

Abdul Wadood et al.

Summary: The study aimed to identify inhibitors that could bind to the mutant state of the RpsA protein in pyrazinoic acid-resistant tuberculosis using virtual screening and molecular dynamics study to find useful compounds.

ACS OMEGA (2022)

Article Biochemistry & Molecular Biology

Predicting Multi-Interfacial Binding Mechanisms of NLRP3 and ASC Pyrin Domains in Inflammasome Activation

Muhammad Riaz et al.

Summary: The NLRP3-PYD inflammasome activates an inflammatory pathway in response to cell damage or infections, with dysregulation leading to chronic inflammation and autoimmune disorders. Computational approaches were used to study the interactions of NLRP3 and ASC PYD domains involved in inflammasome complex activation. The research sheds light on the molecular mechanisms of inflammasome and offers insights into drug discovery processes.

ACS CHEMICAL NEUROSCIENCE (2021)

Article Genetics & Heredity

Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers

Corina Lesseur et al.

Summary: Squamous cell carcinomas (SqCC) of the aerodigestive tract share common etiological risk factors and genetic susceptibility. A meta-analysis of GWAS data identified novel and pleiotropic risk variants, highlighting the importance of cross-cancer analyses. Gene-based association and gene set enrichment revealed SqCC-related genes involved in DNA damage and epigenetic regulation pathways. The study suggests overlap in genetic factors influencing aerodigestive SqCC risk in European populations.

PLOS GENETICS (2021)

Article Biochemistry & Molecular Biology

PRMT1 promotes the tumor suppressor function of p14ARF and is indicative for pancreatic cancer prognosis

Antje Repenning et al.

Summary: The study reveals that PRMT1-mediated arginine methylation is crucial for triggering stress-induced tumor-suppressive function of p14(ARF). The interaction between PRMT1 and p14(ARF) leads to the release of p14(ARF) from nucleoli, promoting p53-independent apoptosis in response to genotoxic stress. This cooperation between PRMT1 and p14(ARF) has implications for cancer prognosis and chemotherapy response in pancreatic ductal adenocarcinoma.

EMBO JOURNAL (2021)

Article Biochemistry & Molecular Biology

Sequencing and comparative genome analysis of three Indians

Harish Padh

Summary: Advancements in DNA sequencing technology have made personal genome analysis feasible and affordable. The whole genome sequencing and analysis of three individuals from different parts of India revealed a significant number of new variants, indicating the complexity of Indian population admix developed from several distinct waves of human migration.

MAMMALIAN GENOME (2021)

Article Biochemical Research Methods

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

Wei Zheng et al.

Summary: C-I-TASSER protocol combines neural network learning and I-TASSER simulations to predict the structure of proteins lacking homologous templates, showing better performance in large-scale tests. By integrating whole-genome and metagenome information, it successfully addresses the issue of non-homologous protein structure prediction.

CELL REPORTS METHODS (2021)

Letter Dermatology

Novel Frameshift Mutations in XPC Gene Underlie Xeroderma Pigmentosum in Pakistani Families

Ambreen Ijaz et al.

INDIAN JOURNAL OF DERMATOLOGY (2021)

Article Biotechnology & Applied Microbiology

Discovering the mechanism and involvement of the methylation of cyclin-dependent kinase inhibitor 2A (CDKN2A) gene and its special locus region in gastric cancer

Jiye Xu et al.

Summary: The study found that low methylation of the CDKN2A gene was associated with better prognosis in gastric cancer patients, while methylation levels of certain loci were negatively correlated with CDKN2A gene expression. GSEA analysis showed that certain pathways may play a role in the regulation of CDKN2A gene hypermethylation.

BIOENGINEERED (2021)

Review Biochemistry & Molecular Biology

GWAS in cancer: progress and challenges

Baiqiang Liang et al.

MOLECULAR GENETICS AND GENOMICS (2020)

Article Biochemistry & Molecular Biology

Decoding allosteric communication pathways in protein lysine acetyltransferase

Ashfaq Ur Rehman et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2020)

Article Chemistry, Medicinal

Gain-of-Function SHP2 E76Q Mutant Rescuing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia

Ashfaq Ur Rehman et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Oncology

Analysis of CDKN2A gene alterations in recurrent and non-recurrent meningioma

Anne Guyot et al.

JOURNAL OF NEURO-ONCOLOGY (2019)

Article Biochemistry & Molecular Biology

VarCards: an integrated genetic and clinical database for coding variants in the human genome

Jinchen Li et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Victor Lopez-Ferrando et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Physical

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Edward Harder et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Biochemical Research Methods

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

Yongwook Choi et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

I-TASSER server: new development for protein structure and function predictions

Jianyi Yang et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Jaroslav Bendl et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Exploring the genetic basis of chronic periodontitis: a genome-wide association study

Kimon Divaris et al.

HUMAN MOLECULAR GENETICS (2013)

Review Biochemistry & Molecular Biology

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein Protein Interactions

Christopher M. Yates et al.

JOURNAL OF MOLECULAR BIOLOGY (2013)

Article Biochemical Research Methods

Identifying ChIP-seq enrichment using MACS

Jianxing Feng et al.

NATURE PROTOCOLS (2012)

Article Biotechnology & Applied Microbiology

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

Emidio Capriotti et al.

GENOMICS (2011)

Review Cell Biology

Genetic advances in glioma: susceptibility genes and networks

Yanhong Liu et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2010)

Letter Biochemical Research Methods

A method and server for predicting damaging missense mutations

Ivan A. Adzhubei et al.

NATURE METHODS (2010)

Article Biochemistry & Molecular Biology

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Haim Ashkenazy et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

Prateek Kumar et al.

NATURE PROTOCOLS (2009)

Article Biochemistry & Molecular Biology

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Paul D. Thomas et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Identification and analysis of deleterious human SNPs

P Yue et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Prediction of protein stability changes for single-site mutations using support vector machines

JL Cheng et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Biochemical Research Methods

Predicting protein stability changes from sequences using support vector machines

E Capriotti et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

M Landau et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

E Capriotti et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

SIFT: predicting amino acid changes that affect protein function

PC Ng et al.

NUCLEIC ACIDS RESEARCH (2003)