How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?

Inter-residue, inter-protein and inter-family coevolution: bridging the scales

(2018) Hendrik Szurmant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

ACE: adaptive cluster expansion for maximum entropy graphical model inference

(2016) J. P. Barton et al.   BIOINFORMATICS

On the Sufficiency of Pairwise Interactions in Maximum Entropy Models of Networks

(2016) Lina Merchan et al.   JOURNAL OF STATISTICAL PHYSICS

Structural propensities of kinase family proteins from a Potts model of residue co-variation

(2016) Allan Haldane et al.   PROTEIN SCIENCE

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

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

(2011) David T. Jones et al.   BIOINFORMATICS

Are Biological Systems Poised at Criticality?

(2011) Thierry Mora et al.   JOURNAL OF STATISTICAL PHYSICS

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

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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