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

Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions

(2017) Vanessa E. Gray et al.   GENETICS

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

(2017) Vikas Pejaver et al.   HUMAN MUTATION

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

(2017) Roxana Daneshjou et al.   HUMAN MUTATION

Whole-protein alanine-scanning mutagenesis of allostery: A large percentage of a protein can contribute to mechanism

(2017) Qingling Tang et al.   HUMAN MUTATION

Exploring the limits of the usefulness of mutagenesis in studies of allosteric mechanisms

(2017) Qingling Tang et al.   HUMAN MUTATION

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

(2017) Yvonne H. Chan et al.   Nature Communications

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

(2017) M. Miller et al.   Scientific Reports

Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions

(2017) Vanessa E. Gray et al.   GENETICS

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

(2016) Haiming Tang et al.   BIOINFORMATICS

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

(2016) Liskin Swint-Kruse   BIOPHYSICAL JOURNAL

SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations

(2016) Marharyta Petukh et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2016) Monkol Lek et al.   NATURE

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

(2016) David Mavor et al.   eLife

Distinguishing the Interactions in the Fructose 1,6-Bisphosphate Binding Site of Human Liver Pyruvate Kinase That Contribute to Allostery

(2015) Arjun Ishwar et al.   BIOCHEMISTRY

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

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

(2015) Marharyta Petukh et al.   HUMAN MUTATION

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

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

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

(2015) Abhishek Niroula et al.   PLoS One

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

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

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Identification of Regions of Rabbit Muscle Pyruvate Kinase Important for Allosteric Regulation by Phenylalanine, Detected by H/D Exchange Mass Spectrometry

(2013) Charulata B. Prasannan et al.   BIOCHEMISTRY

Collective judgment predicts disease-associated single nucleotide variants

(2013) Emidio Capriotti et al.   BMC GENOMICS

Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein

(2013) Basavanapura N. Gangadhara et al.   JOURNAL OF MOLECULAR BIOLOGY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

Rheostats and Toggle Switches for Modulating Protein Function

(2013) Sarah Meinhardt et al.   PLoS One

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

(2013) Tjaart A. P. de Beer et al.   PLoS Computational Biology

Energetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase

(2012) Todd Holyoak et al.   BIOCHEMISTRY

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations

(2012) V. E. Gray et al.   BIOINFORMATICS

Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression

(2012) Sarah Meinhardt et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

In vivo tests of thermodynamic models of transcription repressor function

(2011) Sudheer Tungtur et al.   BIOPHYSICAL CHEMISTRY

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva 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

Functionally important positions can comprise the majority of a protein's architecture

(2011) Sudheer Tungtur et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

The pH dependence of the allosteric response of human liver pyruvate kinase to fructose-1,6-bisphosphate, ATP, and alanine

(2009) Aron W. Fenton et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Comparing the Functional Roles of Nonconserved Sequence Positions in Homologous Transcription Repressors: Implications for Sequence/Function Analyses

(2009) Sudheer Tungtur et al.   JOURNAL OF MOLECULAR BIOLOGY

Subdividing Repressor Function: DNA Binding Affinity, Selectivity, and Allostery Can Be Altered by Amino Acid Substitution of Nonconserved Residues in a LacI/GalR Homologue†

(2008) Hongli Zhan et al.   BIOCHEMISTRY

Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: Bioinformatics-based predictions generate true positives and false negatives

(2008) Sarah Meinhardt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genetic Variation in an Individual Human Exome

(2008) Pauline C. Ng et al.   PLoS Genetics

Ligand-induced Conformational Changes and Conformational Dynamics in the Solution Structure of the Lactose Repressor Protein

(2007) Marc Taraban et al.   JOURNAL OF MOLECULAR BIOLOGY