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RECOMB
2004
Springer
14 years 7 months ago
Mining protein family specific residue packing patterns from protein structure graphs
Finding recurring residue packing patterns, or spatial motifs, that characterize protein structural families is an important problem in bioinformatics. To this end, we apply a nov...
Jun Huan, Wei Wang 0010, Deepak Bandyopadhyay, Jac...
WABI
2001
Springer
142views Bioinformatics» more  WABI 2001»
13 years 12 months ago
Pattern Matching and Pattern Discovery Algorithms for Protein Topologies
We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgrap...
Juris Viksna, David Gilbert
BMCBI
2010
167views more  BMCBI 2010»
13 years 7 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
JCB
2000
71views more  JCB 2000»
13 years 7 months ago
Structure Comparison and Structure Patterns
This article investigates aspects of pairwise and multiple structure comparison, and the problem of automatically discover common patterns in a set of structures. Descriptions and...
Ingvar Eidhammer, Inge Jonassen, William R. Taylor
PRL
2011
12 years 10 months ago
Structural matching of 2D electrophoresis gels using deformed graphs
2D electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. Each spot in the image represents a protein accumulation an...
Alexandre Noma, Alvaro Pardo, Roberto Marcondes Ce...