Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning

Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area

(2019) Yan He et al.   PLoS One

Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations

(2019) Nidhi Jatana et al.   Autophagy

Exploring Gatekeeper Mutations in EGFR through Computer Simulations

(2019) Srinivasaraghavan Kannan et al.   Journal of Chemical Information and Modeling

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

(2019) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Synthesis and Structure–Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH

(2019) Vinayak Singh et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census

(2019) Sony Malhotra et al.   PLoS One

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India

(2019) Asma Munir et al.   Scientific Reports

Insights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations

(2019) Budheswar Dehury et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A missense mutation in SLC6A1 associated with Lennox-Gastaut syndrome impairs GABA transporter 1 protein trafficking and function

(2019) Kefu Cai et al.   EXPERIMENTAL NEUROLOGY

Quantification of biases in predictions of protein stability changes upon mutations

(2018) Fabrizio Pucci et al.   BIOINFORMATICS

SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

(2018) Justina Jankauskaitė et al.   BIOINFORMATICS

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

(2018) Kathryn E. Holt et al.   NATURE GENETICS

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

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

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

(2018) Sundeep Chaitanya Vedithi et al.   Scientific Reports

ClinVar at five years: Delivering on the promise

(2018) Melissa J. Landrum et al.   HUMAN MUTATION

Investigation of deleterious effects of nsSNPs in the POT1 gene: a structural genomics‐based approach to understand the mechanism of cancer development

(2018) Mohd. Amir et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

(2017) Daniele Raimondi et al.   NUCLEIC ACIDS RESEARCH

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

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

SDM: a server for predicting effects of mutations on protein stability

(2017) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions

(2017) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health

(2017) Harry C. Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects

(2016) Daniele Raimondi et al.   BIOINFORMATICS

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

(2016) Haiming Tang et al.   BIOINFORMATICS

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

(2016) Jody Phelan et al.   BMC Medicine

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

(2016) Abhishek Niroula et al.   HUMAN MUTATION

Computational approaches for predicting mutant protein stability

(2016) Shweta Kulshreshtha et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Next generation sequencing: implications in personalized medicine and pharmacogenomics

(2016) Bahareh Rabbani et al.   Molecular BioSystems

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance

(2016) Douglas E. V. Pires et al.   Scientific Reports

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis

(2016) Vinayak Singh et al.   ACS Infectious Diseases

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

(2016) Douglas E. V. Pires et al.   Scientific Reports

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

(2015) Piero Fariselli et al.   BIOINFORMATICS

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

(2015) Yongwook Choi et al.   BIOINFORMATICS

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy

(2015) Martina Nemethova et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

VariSNP, A Benchmark Database for Variations From dbSNP

(2015) Gerard C.P. Schaafsma et al.   HUMAN MUTATION

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Network effects of disease mutations

(2015) Darren J. Burgess   NATURE REVIEWS GENETICS

Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma

(2015) M. Jafri et al.   Cancer Discovery

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

(2014) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes

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

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

Computational approaches to interpreting genomic sequence variation

(2014) Graham RS Ritchie et al.   Genome Medicine

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Bioinformatics analysis of the epitope regions for norovirus capsid protein

(2013) Liping Chen et al.   BMC BIOINFORMATICS

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

(2013) S. Castellana et al.   BRIEFINGS IN BIOINFORMATICS

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

(2013) Kuan Pern Tan et al.   NUCLEIC ACIDS RESEARCH

Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies

(2013) Miao-Xin Li et al.   PLoS Genetics

PON-P: Integrated predictor for pathogenicity of missense variants

(2012) Ayodeji Olatubosun et al.   HUMAN MUTATION

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

PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes

(2012) Yunqi Li et al.   PLoS One

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site

(2011) Gilad Wainreb et al.   BIOINFORMATICS

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

(2011) Douglas EV Pires et al.   BMC GENOMICS

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

The linear interaction energy method for the prediction of protein stability changes upon mutation

(2011) Lauren Wickstrom et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prots: A fragment based protein thermo-stability potential

(2011) Yunqi Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

(2010) Shaolei Teng et al.   BMC GENOMICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

(2010) M. Masso et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Integrated prediction of the effect of mutations on multiple protein characteristics

(2010) Michael A. Johnston et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li 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

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis

(2009) Julia R. Forman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis

(2008) M. Masso et al.   BIOINFORMATICS

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE