Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity

Statistical investigations of protein residue direct couplings

(2019) Andrew F. Neuwald et al.   PLoS Computational Biology

Revealing evolutionary constraints on proteins through sequence analysis

(2019) Shou-Wen Wang et al.   PLoS Computational Biology

The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes

(2019) Faruck Morcos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Inferring joint sequence-structural determinants of protein functional specificity

(2018) Andrew F Neuwald et al.   eLife

PHOTOPHYSICAL CHARACTERIZATION OF INTERCHROMOPHORIC INTERACTIONS BETWEEN RHODAMINE DYES CONJUGATED TO PROTEINS.

(2018) Bryan Donaphon et al.   Methods and Applications in Fluorescence

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information

(2017) Priyadarshini P. Pai et al.   Molecular Informatics

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations

(2016) Andrew F. Neuwald et al.   PLoS Computational Biology

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Protein Sectors: Statistical Coupling Analysis versus Conservation

(2015) Tiberiu Teşileanu et al.   PLoS Computational Biology

PINGU: PredIction of eNzyme catalytic residues usinG seqUence information

(2015) Priyadarshini P. Pai et al.   PLoS One

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

(2014) Yuxiang Jiang et al.   BIOINFORMATICS

H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments

(2014) Jan-Oliver Janda et al.   BMC BIOINFORMATICS

A survey on prediction of specificity-determining sites in proteins

(2014) A. Chakraborty et al.   BRIEFINGS IN BIOINFORMATICS

A Bayesian Sampler for Optimization of Protein Domain Hierarchies

(2014) Andrew F. Neuwald   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

Protein domain hierarchy Gibbs sampling strategies

(2014) Andrew F. Neuwald   Statistical Applications in Genetics and Molecular Biology

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis

(2013) Ajay Singh Tanwar et al.   PLoS One

CAFA and the Open World of protein function predictions

(2013) Christophe Dessimoz et al.   TRENDS IN GENETICS

Replication Clamps and Clamp Loaders

(2013) M. Hedglin et al.   Cold Spring Harbor Perspectives in Biology

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

(2013) Simona Cocco et al.   PLoS Computational Biology

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

(2012) Jan-Oliver Janda et al.   BMC BIOINFORMATICS

Clamp loader ATPases and the evolution of DNA replication machinery

(2012) Brian A Kelch et al.   BMC BIOLOGY

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

The β Sliding Clamp Closes around DNA prior to Release by theEscherichia coliClamp Loader γ Complex

(2012) Jaclyn N. Hayner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Replicases from a Bacterial Perspective

(2011) Charles S. McHenry   Annual Review of Biochemistry

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Computational Methods for Identification of Functional Residues in Protein Structures

(2011) Fuxiao Xin et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

The Escherichia coli Clamp Loader Can Actively Pry Open the β-Sliding Clamp

(2011) Christopher O. Paschall et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How a DNA Polymerase Clamp Loader Opens a Sliding Clamp

(2011) B. A. Kelch et al.   SCIENCE

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences

(2009) Andrew F. Neuwald   BIOINFORMATICS

Ensemble approach to predict specificity determinants: benchmarking and validation

(2009) Saikat Chakrabarti et al.   BMC BIOINFORMATICS

Combining specificity determining and conserved residues improves functional site prediction

(2009) Olga V Kalinina et al.   BMC BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

The Mechanism of ATP-Dependent Primer-Template Recognition by a Clamp Loader Complex

(2009) Kyle R. Simonetta et al.   CELL

A Slow ATP-induced Conformational Change Limits the Rate of DNA Binding but Not the Rate of β Clamp Binding by the Escherichia coli γ Complex Clamp Loader

(2009) Jennifer A. Thompson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification

(2008) Sriram Sankararaman et al.   BIOINFORMATICS

Characterization and prediction of residues determining protein functional specificity

(2008) John A. Capra et al.   BIOINFORMATICS

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA