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JCC
2011
154views more  JCC 2011»
10 years 9 months ago
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
: Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the ...
Dariusz Plewczynski, Michal Lazniewski, Rafal Augu...
BMCBI
2010
123views more  BMCBI 2010»
11 years 1 months ago
Predicting conserved protein motifs with Sub-HMMs
Background: Profile HMMs (hidden Markov models) provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is th...
Kevin Horan, Christian R. Shelton, Thomas Girke
BMCBI
2005
99views more  BMCBI 2005»
11 years 6 months ago
Super paramagnetic clustering of protein sequences
Background: Detection of sequence homologues represents a challenging task that is important for the discovery of protein families and the reliable application of automatic annota...
Igor V. Tetko, Axel Facius, Andreas Ruepp, Hans-We...
BMCBI
2005
97views more  BMCBI 2005»
11 years 6 months ago
Clustering the annotation space of proteins
Background: Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas. Results: Her...
Victor Kunin, Christos A. Ouzounis
BMCBI
2005
149views more  BMCBI 2005»
11 years 6 months ago
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional pre
Background: The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is o...
Jan Kosinski, Marcin Feder, Janusz M. Bujnicki
BMCBI
2005
119views more  BMCBI 2005»
11 years 6 months ago
The distance-profile representation and its application to detection of distantly related protein families
Background: Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized protei...
Chin-Jen Ku, Golan Yona
JCB
2006
185views more  JCB 2006»
11 years 6 months ago
Identification of Amino Acid Latent Periodicity within 94 Protein Families
Here, we have applied information decomposition, cyclic profile alignment, and noise decomposition techniques to search for latent repeats within protein families of various funct...
Vera P. Turutina, Andrew A. Laskin, Nikolay A. Kud...
BMCBI
2007
116views more  BMCBI 2007»
11 years 6 months ago
Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases
Background: The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evoluti...
César L. Avila, Viviana A. Rapisarda, Ricar...
BMCBI
2006
202views more  BMCBI 2006»
11 years 6 months ago
DWARF - a data warehouse system for analyzing protein families
Background: The emerging field of integrative bioinformatics provides the tools to organize and systematically analyze vast amounts of highly diverse biological data and thus allo...
Markus Fischer, Quan K. Thai, Melanie Grieb, J&uum...
GECCO
2005
Springer
162views Optimization» more  GECCO 2005»
12 years 4 days ago
Discovering biological motifs with genetic programming
Choosing the right representation for a problem is important. In this article we introduce a linear genetic programming approach for motif discovery in protein families, and we al...
Rolv Seehuus, Amund Tveit, Ole Edsberg
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