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

Entropy-driven partitioning of the hierarchical protein space

(2014) N. Rappoport et al.   BIOINFORMATICS

A survey on prediction of specificity-determining sites in proteins

(2014) A. Chakraborty et al.   BRIEFINGS IN BIOINFORMATICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Functional site plasticity in domain superfamilies

(2013) Benoit H. Dessailly et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Bioinformatics analysis of the epitope regions for norovirus capsid protein

(2013) Liping Chen et al.   BMC BIOINFORMATICS

Top-Down Clustering for Protein Subfamily Identification

(2013) Eduardo P. Costa et al.   Evolutionary Bioinformatics

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

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis

(2013) Jonathan G. Lees et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

(2013) Alexandra M. Schnoes et al.   PLoS Computational Biology

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

(2012) Limin Fu et al.   BIOINFORMATICS

TIGRFAMs and Genome Properties in 2013

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

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Evolutionarily consistent families in SCOP: sequence, structure and function

(2012) Ralph B Pethica et al.   BMC STRUCTURAL BIOLOGY

Quality of Computationally Inferred Gene Ontology Annotations

(2012) Nives Škunca et al.   PLoS Computational Biology

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

(2010) Pavel V Mazin et al.   Algorithms for Molecular Biology

A fast and automated solution for accurately resolving protein domain architectures

(2010) Corin Yeats et al.   BIOINFORMATICS

The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations

(2010) Michael Widmann et al.   BMC BIOCHEMISTRY

SUPERFAMILY 1.75 including a domain-centric gene ontology method

(2010) D. A. de Lima Morais et al.   NUCLEIC ACIDS RESEARCH

Protein interactions and ligand binding: From protein subfamilies to functional specificity

(2010) A. Rausell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting structural classifications for function prediction: towards a domain grammar for protein function

(2009) Benoît H Dessailly et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

(2009) David A. Lee et al.   NUCLEIC ACIDS RESEARCH

Profile Comparer: a program for scoring and aligning profile hidden Markov models

(2008) M. Madera   BIOINFORMATICS

Characterization and prediction of residues determining protein functional specificity

(2008) John A. Capra et al.   BIOINFORMATICS

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

(2008) T. Lima et al.   NUCLEIC ACIDS RESEARCH