Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers

Improved enzyme annotation with EC-specific cutoffs using DETECT v2

(2018) Nirvana Nursimulu et al.   BIOINFORMATICS

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

(2018) Alperen Dalkiran et al.   BMC BIOINFORMATICS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

(2017) Jae Yong Ryu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human protein atlas: A spatial map of the human proteome

(2017) Peter J. Thul et al.   PROTEIN SCIENCE

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

(2016) Ying Hong Li et al.   PLoS One

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

(2016) Daniel Machado et al.   PLoS Computational Biology

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

EnzDP: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles

(2015) Nam-Ninh Nguyen et al.   Journal of Bioinformatics and Computational Biology

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

(2012) Narendra Kumar et al.   BIOINFORMATICS

EnzML: multi-label prediction of enzyme classes using InterPro signatures

(2012) Luna De Ferrari et al.   BMC BIOINFORMATICS

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Computational framework for predictive biodegradation

(2009) Stacey D. Finley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-wide enzyme annotation with precision control: Catalytic families (CatFam) databases

(2008) Chenggang Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS