Environmental conditions shape the nature of a minimal bacterial genome

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene3D: Extensive prediction of globular domains in proteins

(2017) Tony E Lewis et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Unknown unknowns: essential genes in quest for function

(2016) Antoine Danchin et al.   Microbial Biotechnology

FFPred 3: feature-based function prediction for all Gene Ontology domains

(2016) Domenico Cozzetto et al.   Scientific Reports

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

(2015) Sayoni Das et al.   BIOINFORMATICS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps

(2015) Yi-Chien Chang et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

The SUPERFAMILY 1.75 database in 2014: a doubling of data

(2014) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

LocTree3 prediction of localization

(2014) Tatyana Goldberg et al.   NUCLEIC ACIDS RESEARCH

HAMAP in 2015: updates to the protein family classification and annotation system

(2014) Ivo Pedruzzi et al.   NUCLEIC ACIDS RESEARCH

Prediction of Membrane Transport Proteins and Their Substrate Specificities Using Primary Sequence Information

(2014) Nitish K. Mishra et al.   PLoS One

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

The Structure–Function Linkage Database

(2013) Eyal Akiva et al.   NUCLEIC ACIDS RESEARCH

DOOR 2.0: presenting operons and their functions through dynamic and integrated views

(2013) Xizeng Mao et al.   NUCLEIC ACIDS RESEARCH

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

(2012) Marco Falda et al.   BMC BIOINFORMATICS

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

(2012) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

CombFunc: predicting protein function using heterogeneous data sources

(2012) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

firestar —advances in the prediction of functionally important residues

(2011) Gonzalo Lopez et al.   NUCLEIC ACIDS RESEARCH

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

ConFunc—functional annotation in the twilight zone

(2008) Mark N. Wass et al.   BIOINFORMATICS