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» Computing with Evolving Proteins
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BMCBI
2007
216views more  BMCBI 2007»
14 years 9 months ago
A replica exchange Monte Carlo algorithm for protein folding in the HP model
Background: The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of...
Chris Thachuk, Alena Shmygelska, Holger H. Hoos
BMCBI
2007
93views more  BMCBI 2007»
14 years 9 months ago
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
Background: Predicting a protein’s structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing ne...
Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, W...
BMCBI
2007
115views more  BMCBI 2007»
14 years 9 months ago
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
Background: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples ...
Gabriele Ausiello, Daniele Peluso, Allegra Via, Ma...
BMCBI
2005
151views more  BMCBI 2005»
14 years 9 months ago
ProMiner: rule-based protein and gene entity recognition
Background: Identification of gene and protein names in biomedical text is a challenging task as the corresponding nomenclature has evolved over time. This has led to multiple syn...
Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevis...
BMCBI
2008
128views more  BMCBI 2008»
14 years 10 months ago
An efficient visualization tool for the analysis of protein mutation matrices
Background: It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce eithe...
Maria Pamela C. David, Carlo M. Lapid, Vincent Ric...