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» Local Search Heuristic for Rigid Protein Docking
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COMPGEOM
2004
ACM
13 years 10 months ago
Extreme elevation on a 2-manifold
Given a smoothly embedded 2-manifold in ¤¦¥ , we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our de...
Pankaj K. Agarwal, Herbert Edelsbrunner, John Hare...
PRIB
2009
Springer
120views Bioinformatics» more  PRIB 2009»
13 years 11 months ago
Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands
Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling. We present a knowledge-guided approach for docking protein dom...
Haiyun Lu, Hao Li, Shamima Banu Bte Sm Rashid, Wee...
WEA
2009
Springer
126views Algorithms» more  WEA 2009»
13 years 11 months ago
Computing Elevation Maxima by Searching the Gauss Sphere
The elevation function on a smoothly embedded 2-manifold in R3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in iden...
Bei Wang, Herbert Edelsbrunner, Dmitriy Morozov
BMCBI
2010
116views more  BMCBI 2010»
13 years 5 months ago
A hybrid approach to protein folding problem integrating constraint programming with local search
Background: The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy func...
Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel
DATESO
2007
157views Database» more  DATESO 2007»
13 years 6 months ago
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases
When searching databases of nucleotide or protein sequences, finding a local alignment of two sequences is one of the main tasks. Since the sizes of available databases grow const...
David Hoksza, Tomás Skopal