Identification of the most damaging nsSNPs in the human CFL1 gene and their functional and structural impacts on cofilin-1 protein

In silico analysis of non-synonymous missense SNPs (nsSNPs) in CPE, GNAS genes and experimental validation in type II diabetes mellitus through Next Generation Sequencing

(2021) Bibi Sabiha et al.   GENOMICS

Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6

(2021) Tianqi Gong et al.   MOLECULES

Designing a multi-epitope vaccine candidate to combat MERS-CoV by employing an immunoinformatics approach

(2021) Shafi Mahmud et al.   Scientific Reports

In silico search of triple mutant T790M/C797S allosteric inhibitors to conquer acquired resistance problem in non-small cell lung cancer (NSCLC): a combined approach of structure-based virtual screening and molecular dynamics simulation

(2020) Harun M. Patel et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Silico Elucidation of Deleterious Non-synonymous SNPs in SHANK3, the Autism Spectrum Disorder Gene

(2020) Hajar Owji et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Mutational analysis on predicting the impact of high-risk SNPs in human secretary phospholipase A2 receptor (PLA2R1)

(2020) Zoya Khalid et al.   Scientific Reports

Estimation of varicocele associated human ARG2 and NOS1 proteins and computational analysis on the effect of its nsSNPs

(2020) Vyshali Karthikeyan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Role of Cofilin in Alzheimer’s Disease

(2020) Qiang Wang et al.   Frontiers in Cell and Developmental Biology

Methods for the Refinement of Protein Structure 3D Models

(2019) Adiyaman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

(2019) Gyu Rie Lee et al.   NUCLEIC ACIDS RESEARCH

Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation

(2019) Md. Jahirul Islam et al.   Scientific Reports

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Non-Conjugated Chitosan-Based Nanoparticles to Proteic Antigens Elicit Similar Humoral Immune Responses to Those Obtained with Alum

(2017) I. Y Izaguirre-Hernández et al.   JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

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

(2017) Víctor López-Ferrando et al.   NUCLEIC ACIDS RESEARCH

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants

(2017) Emidio Capriotti et al.   NUCLEIC ACIDS RESEARCH

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment

(2017) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

What makes it difficult to refine protein models further via molecular dynamics simulations?

(2017) Lim Heo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

INPS-MD: a web server to predict stability of protein variants from sequence and structure: Table 1.

(2016) Castrense Savojardo et al.   BIOINFORMATICS

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Describing the Prevalence of Neural Tube Defects Worldwide: A Systematic Literature Review

(2016) Ibrahim Zaganjor et al.   PLoS One

INPS: predicting the impact of non-synonymous variations on protein stability from sequence

(2015) Piero Fariselli et al.   BIOINFORMATICS

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification

(2015) Yul Kim et al.   BMC Medical Genomics

ADF/cofilin: a crucial regulator of synapse physiology and behavior

(2015) Marco B. Rust   CELLULAR AND MOLECULAR LIFE SCIENCES

Roles of cofilin in development and its mechanisms of regulation

(2015) Kazumasa Ohashi   DEVELOPMENT GROWTH & DIFFERENTIATION

Computational analyses and prediction of guanylin deleterious SNPs

(2015) William F. Porto et al.   PEPTIDES

Overexpression of cofilin 1 in prostate cancer and the corresponding clinical implications

(2015) LI LU et al.   Oncology Letters

Generation of contractile actomyosin bundles depends on mechanosensitive actin filament assembly and disassembly

(2015) Sari Tojkander et al.   eLife

PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants

(2015) Abhishek Niroula et al.   PLoS One

Neural Tube Defects

(2014) Nicholas D.E. Greene et al.   Annual Review of Neuroscience

14-3-3 Proteins Are Required for Hippocampal Long-Term Potentiation and Associative Learning and Memory

(2014) H. Qiao et al.   JOURNAL OF NEUROSCIENCE

Significance of 5,10-methylenetetrahydrofolate reductase gene variants in acute lymphoblastic leukemia in Indian population: an experimental, computational and meta-analysis

(2014) Ravishankara Bellampalli et al.   LEUKEMIA & LYMPHOMA

Cofilin/Actin Rod Formation by Dysregulation of Cofilin-1 Activity as a Central Initial Step in Neurodegeneration

(2014) Patricia Schonhofen et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs

(2014) David Gfeller et al.   PLoS One

Analysis of the human cofilin 1 structure reveals conformational changes required for actin binding

(2013) Marta Klejnot et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology

(2013) Catharina Steentoft et al.   EMBO JOURNAL

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

(2013) Gershon Celniker et al.   ISRAEL JOURNAL OF CHEMISTRY

GalaxyRefine: protein structure refinement driven by side-chain repacking

(2013) Lim Heo et al.   NUCLEIC ACIDS RESEARCH

Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase

(2013) Abdelmonaem Messaoudi et al.   Theoretical Biology and Medical Modelling

Analyzing Effects of Naturally Occurring Missense Mutations

(2012) Zhe Zhang et al.   Computational and Mathematical Methods in Medicine

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Cofilin under control of  -arrestin-2 in NMDA-dependent dendritic spine plasticity, long-term depression (LTD), and learning

(2012) C. G. Pontrello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery

(2011) James T.L. Mah et al.   DRUG DISCOVERY TODAY

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs

(2011) Alessia David et al.   HUMAN MUTATION

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

(2010) Hanka Venselaar et al.   BMC BIOINFORMATICS

Learning, AMPA receptor mobility and synaptic plasticity depend on n-cofilin-mediated actin dynamics

(2010) Marco B Rust et al.   EMBO JOURNAL

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Non-Synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association

(2010) Rong Chen et al.   PLoS One

Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains

(2010) Libusha Kelly et al.   PROTEIN SCIENCE

Defining mechanisms of actin polymerization and depolymerization during dendritic spine morphogenesis

(2009) Pirta Hotulainen et al.   JOURNAL OF CELL BIOLOGY

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

(2009) Prateek Kumar et al.   Nature Protocols

Genetic Basis of Neural Tube Defects

(2009) Alexander G. Bassuk et al.   Seminars in Pediatric Neurology