Evaluation of residue-residue contact prediction in CASP10

Emerging methods in protein co-evolution

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

CASP10 results compared to those of previous CASP experiments

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Definition and classification of evaluation units for CASP10

(2013) Todd J. Taylor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting residue–residue contacts using random forest models

(2011) Yunqi Li et al.   BIOINFORMATICS

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

Evaluation of residue-residue contact predictions in CASP9

(2011) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of disorder predictions in CASP9

(2011) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions

(2011) Sitao Wu et al.   STRUCTURE

MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8

(2010) Z. Wang et al.   BIOINFORMATICS

Effects of site-directed mutagenesis of mglA on motility and swarming of Myxococcus xanthus

(2010) Sarah A Fremgen et al.   BMC MICROBIOLOGY

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

(2010) Lukas Burger et al.   PLoS Computational Biology

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue–residue contacts

(2009) Patrik Björkholm et al.   BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

SAM-T08, HMM-based protein structure prediction

(2009) K. Karplus   NUCLEIC ACIDS RESEARCH

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8

(2009) Iakes Ezkurdia et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

(2008) Marco Vassura et al.   BIOINFORMATICS

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

(2008) Sitao Wu 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

Predicting Key Long-Range Interaction Sites by B-Factors

(2008) Peng Chen et al.   PROTEIN AND PEPTIDE LETTERS

Predicting residue-residue contact maps by a two-layer, integrated neural-network method

(2008) Bin Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of topological contacts in proteins using learning classifier systems

(2008) Michael Stout et al.   SOFT COMPUTING