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» Protein Annotation by Secondary Structure Based Alignments (...
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BMCBI
2008
142views more  BMCBI 2008»
13 years 7 months ago
Strategies for measuring evolutionary conservation of RNA secondary structures
Background: Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for predic...
Andreas R. Gruber, Stephan H. F. Bernhart, Ivo L. ...
NAR
2008
119views more  NAR 2008»
13 years 7 months ago
MALISAM: a database of structurally analogous motifs in proteins
MALISAM (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. To find reliable analogs, ...
Hua Cheng, Bong-Hyun Kim, Nick V. Grishin
BMCBI
2006
103views more  BMCBI 2006»
13 years 7 months ago
Domain-based small molecule binding site annotation
Background: Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule bindi...
Kevin A. Snyder, Howard J. Feldman, Michel Dumonti...
CIKM
2009
Springer
14 years 2 months ago
Linear predictive coding representation of correlated mutation for protein sequence alignment
Background: Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of ali...
Chan-seok Jeong, Dongsup Kim
NAR
2007
136views more  NAR 2007»
13 years 7 months ago
DBAli tools: mining the protein structure space
The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools...
Marc A. Martí-Renom, Ursula Pieper, Mallur ...