When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14 —( tFold for CASP14 contact prediction)

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks

(2019) Yang Li et al.   BIOINFORMATICS

AlphaFold at CASP13

(2019) Mohammed AlQuraishi   BIOINFORMATICS

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

Estimation of model accuracy in CASP13

(2019) Jianlin Cheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Assessing the accuracy of contact predictions in CASP13

(2019) Rojan Shrestha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

(2019) Joe G. Greener et al.   Nature Communications

Protein threading using residue co-variation and deep learning

(2018) Jianwei Zhu et al.   BIOINFORMATICS

CONFOLD2: improved contact-driven ab initio protein structure modeling

(2018) Badri Adhikari et al.   BMC BIOINFORMATICS

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

(2017) Jürgen Haas 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

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

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

(2013) Valerio Mariani et al.   BIOINFORMATICS

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

A conditional neural fields model for protein threading

(2012) Jianzhu Ma 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

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH