funtrp: identifying protein positions for variation driven functional tuning

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

(2019) Vikas Pejaver et al.   HUMAN MUTATION

What went wrong with variant effect predictor performance for the PCM1 challenge

(2019) Maximilian Miller et al.   HUMAN MUTATION

Performance of computational methods for the evaluation of Pericentriolar Material 1 missense variants in CAGI-5

(2019) Alexander Miguel Monzon et al.   HUMAN MUTATION

HFSP: high speed homology-driven function annotation of proteins

(2018) Yannick Mahlich et al.   BIOINFORMATICS

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

(2018) Vanessa E. Gray et al.   Cell Systems

RheoScale: A tool to aggregate and quantify experimentally determined substitution outcomes for multiple variants at individual protein positions

(2018) Abby M. Hodges et al.   HUMAN MUTATION

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

(2017) António J M Ribeiro et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Jinchen Li et al.   NUCLEIC ACIDS RESEARCH

Computational predictors fail to identify amino acid substitution effects at rheostat positions

(2017) M. Miller et al.   Scientific Reports

Identification of metal ion binding sites based on amino acid sequences

(2017) Xiaoyong Cao et al.   PLoS One

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Disease-causing point-mutations in metal-binding domains of Wilson disease protein decrease stability and increase structural dynamics

(2016) Ranjeet Kumar et al.   BIOMETALS

Using Evolution to Guide Protein Engineering: The Devil IS in the Details

(2016) Liskin Swint-Kruse   BIOPHYSICAL JOURNAL

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

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function

(2016) Parul Mishra et al.   Cell Reports

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

Actionable exomic incidental findings in 6503 participants: challenges of variant classification

(2015) Laura M. Amendola et al.   GENOME RESEARCH

The end of the start for population sequencing

(2015) Ewan Birney et al.   NATURE

High-throughput identification of protein mutant stability computed from a double mutant fitness landscape

(2015) Nicholas C. Wu et al.   PROTEIN SCIENCE

Targeted mutagenesis in soybean using the CRISPR-Cas9 system

(2015) Xianjun Sun et al.   Scientific Reports

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

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

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

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

PredictProtein—an open resource for online prediction of protein structural and functional features

(2014) Guy Yachdav et al.   NUCLEIC ACIDS RESEARCH

Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes

(2013) Michael O. Dorschner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

(2013) Romain A. Studer et al.   BIOCHEMICAL JOURNAL

CRAVAT: cancer-related analysis of variants toolkit

(2013) Christopher Douville et al.   BIOINFORMATICS

Collective judgment predicts disease-associated single nucleotide variants

(2013) Emidio Capriotti et al.   BMC GENOMICS

Point mutations as a source of de novo genetic disease

(2013) Joep de Ligt et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Association Between Variants of PRDM1 and NDP52 and Crohn's Disease, Based on Exome Sequencing and Functional Studies

(2013) David Ellinghaus et al.   GASTROENTEROLOGY

Large Numbers of Genetic Variants Considered to be Pathogenic are Common in Asymptomatic Individuals

(2013) Christopher A. Cassa et al.   HUMAN MUTATION

Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease

(2013) Y. Bromberg   JOURNAL OF MOLECULAR BIOLOGY

Rheostats and Toggle Switches for Modulating Protein Function

(2013) Sarah Meinhardt et al.   PLoS One

Neutral and weakly nonneutral sequence variants may define individuality

(2013) Y. Bromberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

(2013) L. M. Starita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function-based assessment of structural similarity measurements using metal co-factor orientation

(2013) Stefan Senn et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

(2012) Yali Xue et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Mutations in maltose-binding protein that alter affinity and solubility properties

(2010) Iris H. Walker et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

Improved Disorder Prediction by Combination of Orthogonal Approaches

(2009) Avner Schlessinger et al.   PLoS One