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WABI
2005
Springer
14 years 1 months ago
Rotamer-Pair Energy Calculations Using a Trie Data Structure
Abstract. Protein design software places amino acid side chains by precomputing rotamer-pair energies and optimizing rotamer placement. If the software optimizes by rapid stochasti...
Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink
JCDL
2004
ACM
103views Education» more  JCDL 2004»
14 years 1 months ago
Integration of biomedical text and sequence OAI repositories
Archived biomedical literature and sequence data are growing rapidly. The Open Archives Initiative's Protocol for Metadata Harvesting (OAI-PMH) [1] provides a convenient way ...
Yueyu Fu, Javed Mostafa
IPPS
1999
IEEE
13 years 12 months ago
Large Scale Simulation of Parallel Molecular Dynamics
This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the simulation of molecular dynamics designed to handle large proteins in biology....
Pierre-Eric Bernard, Thierry Gautier, Denis Trystr...
ALGORITHMICA
2008
115views more  ALGORITHMICA 2008»
13 years 7 months ago
Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection
Color-coding is a technique to design fixed-parameter algorithms for several NP-complete subgraph isomorphism problems. Somewhat surprisingly, not much work has so far been spent ...
Falk Hüffner, Sebastian Wernicke, Thomas Zich...
CCE
2005
13 years 7 months ago
Numerical simulation of stochastic gene circuits
Armed with increasingly fast supercomputers and greater knowledge of the molecular mechanisms of gene expression, it is now practical to numerically simulate complex networks of r...
Howard Salis, Yiannis N. Kaznessis