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» Identifying Structural Motifs in Proteins
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BMCBI
2006
98views more  BMCBI 2006»
13 years 10 months ago
Optimised amino acid specific weighting factors for unbound protein docking
Background: One of the most challenging aspects of protein-protein docking is the inclusion of flexibility into the docking procedure. We developed a postfilter where the grid-rep...
Philipp Heuser, Dietmar Schomburg
BMCBI
2010
163views more  BMCBI 2010»
13 years 10 months ago
Integration of open access literature into the RCSB Protein Data Bank using BioLit
Background: Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been ...
Andreas Prlic, Marco A. Martinez, Dimitris Dimitro...
BMCBI
2010
137views more  BMCBI 2010»
13 years 10 months ago
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
Background: While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor ...
Michael L. Sierk, Michael E. Smoot, Ellen J. Bass,...
NIPS
2008
13 years 11 months ago
Predicting the Geometry of Metal Binding Sites from Protein Sequence
Metal binding is important for the structural and functional characterization of proteins. Previous prediction efforts have only focused on bonding state, i.e. deciding which prot...
Paolo Frasconi, Andrea Passerini
BMCBI
2010
123views more  BMCBI 2010»
13 years 10 months ago
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
Background: Predicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug desi...
Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe ...