ABSTRACT
BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.
Subject(s)
Databases, Factual , Gene Regulatory Networks , Kinetics , Metabolic Networks and Pathways , Models, Biological , Signal Transduction , Software , User-Computer InterfaceABSTRACT
<p><b>AIM</b>To report the preliminary result of the HIV inhibitor screening based on cheminformatics tools and the traditional Chinese medicine database.</p><p><b>METHODS</b>Database search was carried out with saquinavir molecule as a template, further screening was made with docking. Detailed studies using molecular dynamics simulation of 50 ps and 200 ps were made with respect to a potential leading compound, leucovorin.</p><p><b>RESULTS</b>The leucovorin molecule distinguished from other molecules as a potential drug candidate and is subject to extensive studies. The bonding profile and energy were calculated with MD simulations.</p><p><b>CONCLUSION</b>Our results could be very helpful when we modify leucovorin or design new inhibitors against HIV.</p>