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

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

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

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

Genomics-aided structure prediction

(2012) J. I. Sulkowska 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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

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

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

(2010) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Reducing phylogenetic bias in correlated mutation analysis

(2010) Haim Ashkenazy et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Progress and challenges in predicting protein-protein interaction sites

(2009) I. Ezkurdia et al.   BRIEFINGS IN BIOINFORMATICS

Biophysical dissection of membrane proteins

(2009) Stephen H. White   NATURE

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Using inferred residue contacts to distinguish between correct and incorrect protein models

(2008) Christopher S. Miller 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