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

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

(2019) Mohammed AlQuraishi   BMC BIOINFORMATICS

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

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction

(2018) Ying Xu et al.   Scientific Reports

Single cell RNA-seq data clustering using TF-IDF based methods

(2018) Marmar Moussa et al.   BMC GENOMICS

Dark Proteins Important for Cellular Function

(2018) Andrea Schafferhans et al.   PROTEOMICS

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

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

(2017) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

RaptorX-Property: a web server for protein structure property prediction

(2016) Sheng Wang et al.   NUCLEIC ACIDS RESEARCH

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

(2016) Guillaume Bernard et al.   Scientific Reports

Evolutionary profiles improve protein–protein interaction prediction from sequence

(2015) Tobias Hamp et al.   BIOINFORMATICS

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

(2015) Sikander Hayat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unexpected features of the dark proteome

(2015) Nelson Perdigão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

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

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

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

LocTree2 predicts localization for all domains of life

(2012) Tatyana Goldberg et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Michael Remmert et al.   NATURE METHODS

iLoc-Euk: A Multi-Label Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Eukaryotic Proteins

(2011) Kuo-Chen Chou et al.   PLoS One

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

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

YLoc—an interpretable web server for predicting subcellular localization

(2010) Sebastian Briesemeister et al.   NUCLEIC ACIDS RESEARCH

Neural networks for secondary structure and structural class predictions

(2010) John-Marc Chandonia et al.   PROTEIN SCIENCE

Transmembrane helices predicted at 95% accuracy

(2010) Burkhard Rost et al.   PROTEIN SCIENCE

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

(2010) Cristina Marino Buslje et al.   PLoS Computational Biology

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

(2009) Torsten Blum et al.   BMC BIOINFORMATICS

SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins

(2009) Sebastian Briesemeister et al.   JOURNAL OF PROTEOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Sequence-similar, structure-dissimilar protein pairs in the PDB

(2007) Mickey Kosloff et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS