Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

On the Entropy of Protein Families

(2016) John P. Barton et al.   JOURNAL OF STATISTICAL PHYSICS

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

The network of stabilizing contacts in proteins studied by coevolutionary data

(2013) Sara Lui et al.   JOURNAL OF CHEMICAL PHYSICS

Emerging methods in protein co-evolution

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

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting selection for negative design in proteins through an improved model of the misfolded state

(2013) Jonas Minning et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Adaptive Cluster Expansion for the Inverse Ising Problem: Convergence, Algorithm and Tests

(2012) S. Cocco et al.   JOURNAL OF STATISTICAL PHYSICS

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

(2011) S. Cocco et al.   PHYSICAL REVIEW LETTERS

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

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions

(2011) M. Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins

(2009) Orly Noivirt-Brik et al.   PLoS Computational Biology

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

Interconversion between two unrelated protein folds in the lymphotactin native state

(2008) Robbyn L. Tuinstra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA