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JCC
2008
91views more  JCC 2008»
13 years 7 months ago
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design
Abstract: Our goal is to develop accurate electrostatic models that can be implemented in current computational protein design protocols. To this end, we improve upon a previously ...
Christina L. Vizcarra, Naigong Zhang, Shannon A. M...
SBACPAD
2003
IEEE
138views Hardware» more  SBACPAD 2003»
14 years 22 days ago
Finite Difference Simulations of the Navier-Stokes Equations Using Parallel Distributed Computing
 This paper discusses the implementation of a numerical algorithm for simulating incompressible fluid flows based on the finite difference method and designed for parallel compu...
João Paulo De Angeli, Andréa M. P. V...
BMCBI
2008
128views more  BMCBI 2008»
13 years 7 months ago
Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
Background: Amino acid sequence probability distributions, or profiles, have been used successfully to predict secondary structure and local structure in proteins. Profile models ...
Christopher Bystroff, Bobbie-Jo M. Webb-Robertson
BMCBI
2010
112views more  BMCBI 2010»
13 years 7 months ago
Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design
Background: Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone...
Andrew J. Bordner
HIPC
2009
Springer
13 years 5 months ago
Comparing the performance of clusters, Hadoop, and Active Disks on microarray correlation computations
Abstract--Microarray-based comparative genomic hybridization (aCGH) offers an increasingly fine-grained method for detecting copy number variations in DNA. These copy number variat...
Jeffrey A. Delmerico, Nathanial A. Byrnes, Andrew ...