More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology

Novel eukaryotic enzymes modifying cell-surface biopolymers

(2010) Vivek Anantharaman et al.   Biology Direct

DOG 1.0: illustrator of protein domain structures

(2009) Jian Ren et al.   CELL RESEARCH

Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution

(2009) Ming Ren Yen et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

ANNIE: integrated de novo protein sequence annotation

(2009) H. S. Ooi et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Brichos domain of prosurfactant protein C can hold and fold a transmembrane segment

(2009) Hanna Johansson et al.   PROTEIN SCIENCE

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Deep membrane insertion of prion protein upon reduction of disulfide bond

(2008) Jae-Il Shin et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The effectiveness of position- and composition-specific gap costs for protein similarity searches

(2008) A. Stojmirovic et al.   BIOINFORMATICS

Pfam 10 years on: 10 000 families and still growing

(2008) S. J. Sammut et al.   BRIEFINGS IN BIOINFORMATICS

Membrane Topology and Essential Amino Acid Residues of Phs1, a 3-Hydroxyacyl-CoA Dehydratase Involved in Very Long-chain Fatty Acid Elongation

(2008) Akio Kihara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

PSI-BLAST pseudocounts and the minimum description length principle

(2008) Stephen F. Altschul et al.   NUCLEIC ACIDS RESEARCH

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

CDD: specific functional annotation with the Conserved Domain Database

(2008) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions

(2008) Satoshi Ohnishi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology

Improved detection of homologous membrane proteins by inclusion of information from topology predictions

(2002) Maria Hedman et al.   PROTEIN SCIENCE