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

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

Deep learning

(2015) Yann LeCun et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

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

(2014) David T. Jones et al.   BIOINFORMATICS

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

(2014) Magnus Ekeberg et al.   JOURNAL OF COMPUTATIONAL PHYSICS

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

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Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

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

Predicting protein contact map using evolutionary and physical constraints by integer programming

(2013) Z. Wang et al.   BIOINFORMATICS

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

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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

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Protein Model Portal—a comprehensive resource for protein structure and model information

(2013) Juergen Haas et al.   Database-The Journal of Biological Databases and Curation

Protein structure alignment beyond spatial proximity

(2013) Sheng Wang et al.   Scientific Reports

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

Structure of Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction

(2012) Swarna Mohan et al.   MOLECULAR BIOLOGY OF THE CELL

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

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

(2011) David T. Jones et al.   BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

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

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

(2010) Jinrui Xu et al.   BIOINFORMATICS

Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

(2010) Marcos R. Betancourt et al.   PROTEIN SCIENCE

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