SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model

Improved RNA Secondary Structure and Tertiary Base-pairing Prediction Using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

(2021) Jaswinder Singh et al.   BIOINFORMATICS

SPOT-1D-Single: Improving the Single-Sequence-Based Prediction of Protein Secondary Structure, Backbone Angles, Solvent Accessibility and Half-Sphere Exposures using a Large Training Set and Ensembled Deep Learning

(2021) Jaspreet Singh et al.   BIOINFORMATICS

The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

(2020) Davide Chicco et al.   BMC GENOMICS

SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network

(2020) Ming-Cai Chen et al.   Journal of Chemical Information and Modeling

Protein contact prediction using metagenome sequence data and residual neural networks

(2019) Qi Wu et al.   BIOINFORMATICS

ProteinNet: a standardized data set for machine learning of protein structure

(2019) Mohammed AlQuraishi   BMC 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

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

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

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

(2018) David T Jones et al.   BIOINFORMATICS

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction

(2018) Chao Fang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks

(2018) Jack Hanson et al.   BIOINFORMATICS

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning

(2018) Rhys Heffernan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

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

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

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

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

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

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

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