NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.

PubWeight™: 0.77‹?›

🔗 View Article (PMC 4384005)

Published in Nucleic Acids Res on September 27, 2014

Authors

Richa Mudgal1, Sankaran Sandhya2, Gayatri Kumar3, Ramanathan Sowdhamini4, Nagasuma R Chandra2, Narayanaswamy Srinivasan5

Author Affiliations

1: IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560 012, Karnataka, India.
2: Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India.
3: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India.
4: National Centre for Biological Sciences, Gandhi Krishi Vignan Kendra Campus, Bellary road, Bangalore 560 065, Karnataka, India.
5: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, Karnataka, India ns@mbu.iisc.ernet.in.

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88

Profile hidden Markov models. Bioinformatics (1998) 56.04

The Pfam protein families database. Nucleic Acids Res (2011) 33.46

Pfam: the protein families database. Nucleic Acids Res (2013) 22.48

The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68

UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (2007) 17.43

Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44

The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03

De novo protein design: fully automated sequence selection. Science (1997) 7.86

Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol (1999) 5.90

SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinformatics (2007) 4.19

Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27

Evolutionary information for specifying a protein fold. Nature (2005) 3.23

Intermediate sequences increase the detection of homology between sequences. J Mol Biol (1997) 2.98

De novo protein design: towards fully automated sequence selection. J Mol Biol (1997) 1.84

Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol (2004) 1.48

Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng (1999) 1.47

De novo protein design. I. In search of stability and specificity. J Mol Biol (1999) 1.37

Unification of protein families. Curr Opin Struct Biol (1998) 1.18

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC Bioinformatics (2005) 0.99

Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99

Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. Bioinformatics (2009) 0.97

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res (2006) 0.90

SIMPRO: simple protein homology detection method by using indirect signals. Bioinformatics (2009) 0.90

Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Lett (2003) 0.88

Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. J Mol Biol (2013) 0.79

Improved detection of remote homologues using cascade PSI-BLAST: influence of neighbouring protein families on sequence coverage. PLoS One (2013) 0.78

Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. Mol Biosyst (2012) 0.77