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BMCBI
2010
122views more  BMCBI 2010»
15 years 4 months ago
Fast and accurate protein substructure searching with simulated annealing and GPUs
Background: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioin...
Alex Stivala, Peter J. Stuckey, Anthony Wirth
INTERNET
2007
105views more  INTERNET 2007»
15 years 4 months ago
Workflow Planning on a Grid
evel of abstraction, we can represent a workflow as a directed graph with operators (or tasks) at the vertices (see Figure 1). Each operator takes inputs from data sources or from ...
Craig W. Thompson, Wing Ning Li, Zhichun Xiao
JCC
2007
79views more  JCC 2007»
15 years 3 months ago
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
Abstract: A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with HartreeFock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capab...
H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. ...
115
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JCB
1998
129views more  JCB 1998»
15 years 3 months ago
A Sticker-Based Model for DNA Computation
We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which infor...
Sam T. Roweis, Erik Winfree, Richard Burgoyne, Nic...
SIAMCO
2002
121views more  SIAMCO 2002»
15 years 3 months ago
Consistent Approximations and Approximate Functions and Gradients in Optimal Control
As shown in [7], optimal control problems with either ODE or PDE dynamics can be solved efficiently using a setting of consistent approximations obtained by numerical discretizati...
Olivier Pironneau, Elijah Polak