Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

(2015) Sikander Hayat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CONFOLD: Residue-residue contact-guidedab initioprotein folding

(2015) Badri Adhikari et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PconsFold: improved contact predictions improve protein models

(2014) Mirco Michel et al.   BIOINFORMATICS

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

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

(2014) Sergey Ovchinnikov et al.   eLife

PconsC: combination of direct information methods and alignments improves contact prediction

(2013) Marcin J. Skwark et al.   BIOINFORMATICS

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

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

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) David T. Jones et al.   BIOINFORMATICS

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

Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation

(2011) Oliver F. Lange et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Learning generative models for protein fold families

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

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

(2010) S. Raman et al.   SCIENCE

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

(2010) Lukas Burger et al.   PLoS Computational Biology

Sampling Bottlenecks in De novo Protein Structure Prediction

(2009) David E. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

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