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» Computing with Evolving Proteins
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BMCBI
2011
15 years 1 months ago
Hierarchical graphs for rule-based modeling of biochemical systems
Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state...
Nathan W. Lemons, Bin Hu, William S. Hlavacek
BMCBI
2011
15 years 1 months ago
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling
Background: Molecular database search tools need statistical models to assess the significance for the resulting hits. In the classical approach one asks the question how probable...
Stefan Wolfsheimer, Inke Herms, Sven Rahmann, Alex...
NAR
2011
197views Computer Vision» more  NAR 2011»
14 years 9 months ago
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species
AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, ...
Cristina Aurrecoechea, Ana Barreto, John Brestelli...
NAR
2011
203views Computer Vision» more  NAR 2011»
14 years 9 months ago
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins
The Laminin(LM)-database, hosted at http://www .lm.lncc.br, is the first database focusing a noncollagenous extracellular matrix protein family, the LMs. Part of the knowledge ava...
Daiane C. F. Golbert, Leandra Linhares-Lacerda, Lu...
SC
2009
ACM
16 years 1 months ago
FPGA-based acceleration of CHARMM-potential minimization
Energy minimization is an important step in molecular modeling, with applications in molecular docking and in mapping binding sites. Minimization involves repeated evaluation of v...
Bharat Sukhwani, Martin C. Herbordt