Analysis of several key factors influencing deep learning-based inter-residue contact prediction

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

(2019) Jie Hou 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

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

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Improved protein contact predictions with the MetaPSICOV2 server in CASP12

(2017) Daniel W A Buchan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

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

(2017) Sheng Wang et al.   PLoS Computational Biology

ConEVA: a toolbox for comprehensive assessment of protein contacts

(2016) Badri Adhikari et al.   BMC BIOINFORMATICS

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

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

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC BIOINFORMATICS

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

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

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

Evaluation of residue-residue contact prediction in CASP10

(2013) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt 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

Protein 3D Structure Computed from Evolutionary Sequence Variation

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

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

NNcon: improved protein contact map prediction using 2D-recursive neural networks

(2009) A. N. Tegge et al.   NUCLEIC ACIDS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC 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