On Human Disease-Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns

Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins

(2015) Tugba G Kucukkal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Strong dimerization of wild-type ErbB2/Neu transmembrane domain and the oncogenic Val664Glu mutant in mammalian plasma membranes

(2014) Jesse Placone et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

RAS’s Cloak of Invincibility Slips at Last?

(2014) Julian Downward   CANCER CELL

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

(2014) Tugba Kucukkal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Consequences of the disease-related L78R mutation for dimerization and activity of STAT3

(2014) T. Domoszlai et al.   JOURNAL OF CELL SCIENCE

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

(2014) Minghui Li et al.   Journal of Chemical Theory and Computation

Proper reporting of predictor performance

(2014) Mauno Vihinen   NATURE METHODS

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

Insights from Molecular Dynamics Simulations: Structural Basis for the V567D Mutation-Induced Instability of Zebrafish Alpha-Dystroglycan and Comparison with the Murine Model

(2014) Davide Pirolli et al.   PLoS One

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

(2014) Niklas Berliner et al.   PLoS One

Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2

(2014) Marharyta Petukh et al.   PLoS One

Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs

(2014) Ambuj Kumar et al.   PLoS Computational Biology

Bioinformatics analysis of the epitope regions for norovirus capsid protein

(2013) Liping Chen et al.   BMC BIOINFORMATICS

Computational Screening of Disease-Associated Mutations in OCA2 Gene

(2013) Balu Kamaraj et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Mutation p.S335X in GATA4 Reduces its DNA Binding Affinity and Enhances Cell Apoptosis Associated with Ventricular Septal Defect

(2013) F. Yang et al.   CURRENT MOLECULAR MEDICINE

A Y328C missense mutation in spermine synthase causes a mild form of Snyder–Robinson syndrome

(2013) Zhe Zhang et al.   HUMAN MOLECULAR GENETICS

A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation

(2013) Luigi Boccuto et al.   HUMAN MOLECULAR GENETICS

Understanding Molecular Effects of Naturally Occurring Genetic Differences

(2013) Emil Alexov et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Mechanisms of Disease-Causing Missense Mutations

(2013) Shannon Stefl et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2013) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

(2013) Jonathan M. Ostrem et al.   NATURE

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and Structure

(2013) Clorinda Lori et al.   PLoS One

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

(2013) Hafumi Nishi et al.   PLoS One

The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics

(2013) Qiong Wei et al.   PLoS One

Methionine Mutations of Outer Membrane Protein X Influence Structural Stability and Beta-Barrel Unfolding

(2013) Deepti Chaturvedi et al.   PLoS One

Molecular Dynamic Simulation Reveals Damaging Impact of RAC1 F28L Mutation in the Switch I Region

(2013) Ambuj Kumar et al.   PLoS One

pH-selective mutagenesis of protein-protein interfaces:In silicodesign of therapeutic antibodies with prolonged half-life

(2013) Velin Z. Spassov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Diverse Functional Roles of Reactive Cysteines

(2012) Nicholas J. Pace et al.   ACS Chemical Biology

Predicting folding free energy changes upon single point mutations

(2012) Zhe Zhang et al.   BIOINFORMATICS

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

A New Insight into Structural and Functional Impact of Single-Nucleotide Polymorphisms in PTEN Gene

(2012) C. George Priya Doss et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Analyzing Effects of Naturally Occurring Missense Mutations

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

Computational investigation of pathogenic nsSNPs in CEP63 protein

(2012) Ambuj Kumar et al.   GENE

An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity

(2012) Kyoko Takano et al.   HUMAN MOLECULAR GENETICS

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

Investigating the Structural Impacts of I64T and P311S Mutations in APE1-DNA Complex: A Molecular Dynamics Approach

(2012) C. George Priya Doss et al.   PLoS One

Direct Assessment of the Effect of the Gly380Arg Achondroplasia Mutation on FGFR3 Dimerization Using Quantitative Imaging FRET

(2012) Jesse Placone et al.   PLoS One

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

(2012) Vladimir Vacic et al.   PLoS Computational Biology

In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein

(2011) Vidya Rajendran et al.   AMINO ACIDS

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

Correlating disease-related mutations to their effect on protein stability: A large-scale analysis of the human proteome

(2011) Rita Casadio et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

A257T Linker Region Mutant of T7 Helicase-Primase Protein Is Defective in DNA Loading and Rescued by T7 DNA Polymerase

(2011) Gayatri Patel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

(2011) G. De Baets et al.   NUCLEIC ACIDS RESEARCH

In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in Spermine Synthase

(2011) Zhe Zhang et al.   PLoS One

A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics

(2011) Shawn Witham et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Common Charge-Shift Mutation Glu65Lys in K+ Channel β1-Subunit KCNMB1: Pleiotropic Consequences for Glomerular Filtration Rate and Progressive Renal Disease

(2010) Yuqing Chen et al.   AMERICAN JOURNAL OF NEPHROLOGY

Fanconi anemia group J mutation abolishes its DNA repair function by uncoupling DNA translocation from helicase activity or disruption of protein-DNA complexes

(2010) Y. Wu et al.   BLOOD

Computational analysis of missense mutations causing Snyder-Robinson syndrome

(2010) Zhe Zhang et al.   HUMAN MUTATION

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

Substitution of aspartic acid with glutamic acid at position 67 of the BRCA1 RING domain retains ubiquitin ligase activity and zinc(II) binding with a reduced transition temperature

(2010) Apichart Atipairin et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution

(2010) Emmanuel D. Levy   JOURNAL OF MOLECULAR BIOLOGY

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures

(2009) Michael Ryan et al.   BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions

(2009) Shaolei Teng et al.   BIOPHYSICAL JOURNAL

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Increasing protein stability by improving beta-turns

(2009) Hailong Fu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

(2009) Barbara D'haene et al.   PLoS Genetics

Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results

(2008) Sharon E. Plon et al.   HUMAN MUTATION

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Specific interactions for ab initio folding of protein terminal regions with secondary structures

(2008) Yuedong Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS