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» Comparisons of Protein Family Dynamics
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BMCBI
2004
115views more  BMCBI 2004»
13 years 8 months ago
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
Background: Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed...
Gary W. Stuart, Michael W. Berry
BMCBI
2008
107views more  BMCBI 2008»
13 years 8 months ago
GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2
Background: GPR17 is a G-protein-coupled receptor located at intermediate phylogenetic position between two distinct receptor families: the P2Y and CysLT receptors for extracellul...
Chiara Parravicini, Graziella Ranghino, Maria P. A...
BMCBI
2010
163views more  BMCBI 2010»
13 years 8 months ago
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity
Background: Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeli...
Zong Hong Zhang, Hwee Kuan Lee, Ivana Mihalek
BMCBI
2007
144views more  BMCBI 2007»
13 years 8 months ago
Motif kernel generated by genetic programming improves remote homology and fold detection
Background: Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and ...
Tony Håndstad, Arne J. H. Hestnes, Pål...
BICOB
2010
Springer
14 years 1 months ago
Folding-aware and Structure-conscious 3D Substructures in Folding Data: Identification and Applications
Molecular dynamics simulations have been employed by biologists to study the protein folding problem. Such simulations have resulted in a large number of protein folding trajector...
Hui Yang, Saurabh Gupte, Runtang Wang, Rahul Parte