Improved protein structure prediction using potentials from deep learning

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

(2019) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

(2019) Shaun M. Kandathil et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evaluation of template‐based modeling in CASP13

(2019) Tristan I. Croll et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Analysis of distance‐based protein structure prediction by deep learning in CASP13

(2019) Jinbo Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13

(2019) Yang Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features

(2018) David T Jones et al.   BIOINFORMATICS

Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas

(2018) Melis Kayikci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas

(2018) Melis Kayikci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor

(2018) Martin Audet et al.   Nature Chemical Biology

Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12

(2017) Chengxin Zhang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

(2017) Joerg Schaarschmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2017) Sheng Wang et al.   PLoS Computational Biology

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

(2016) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

Minimum message length inference of secondary structure from protein coordinate data

(2012) A. S. Konagurthu et al.   BIOINFORMATICS

A Position-Specific Distance-Dependent Statistical Potential for Protein Structure and Functional Study

(2012) Feng Zhao et al.   STRUCTURE

An automatic method for CASP9 free modeling structure prediction assessment

(2011) Qian Cong 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

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

(2011) Michael Remmert et al.   NATURE METHODS

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

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics