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» Searching on the Secondary Structure of Protein Sequences
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BMCBI
2010
122views more  BMCBI 2010»
13 years 7 months ago
Fast and accurate protein substructure searching with simulated annealing and GPUs
Background: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioin...
Alex Stivala, Peter J. Stuckey, Anthony Wirth
NAR
2011
208views Computer Vision» more  NAR 2011»
12 years 10 months ago
MIPS: curated databases and comprehensive secondary data resources in 2010
The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotate...
Hans-Werner Mewes, Andreas Ruepp, Fabian J. Theis,...
BMCBI
2008
71views more  BMCBI 2008»
13 years 7 months ago
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible ...
Armita Sheari, Mehdi Kargar, Ali Katanforoush, Sha...
BMCBI
2007
112views more  BMCBI 2007»
13 years 7 months ago
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Background: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to ...
Daniel R. Caffrey, Paul H. Dana, Vidhya Mathur, Ma...
JCB
2007
136views more  JCB 2007»
13 years 7 months ago
A Structure-Based Flexible Search Method for Motifs in RNA
The discovery of non-coding RNA (ncRNA) motifs and their role in regulating gene expression has recently attracted considerable attention. The goal is to discover these motifs in ...
Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny...