Biomedical Engineering Reference
In-Depth Information
Tools
Modeling and simulation are complex operations that tax even the most advanced hardware.
Developing modeling and simulation systems de novo requires knowledge of advanced computing
techniques, from Markov Modeling to network computing and numerical calculus. Fortunately, a wide
variety of modeling simulation tools is available on the Web and from commercial vendors. As listed
in
Table 9-2
, there are tools specifically designed to aid modeling and simulation in bioinformatics as
well as tools for general-purpose modeling. For example, a tool such as Prospect (PROtein Structure
Prediction and Evaluation Computer Toolkit), a threading-based protein structure prediction program,
can be used as part of a comparative modeling process. A commercial system, such as Extend, can
be used to determine the most cost-effective means of staffing the research lab, based on a model of
individual researcher output and the overall protein structure modeling process.
Table 9-2. Modeling and Simulation Tools.
Tool
Examples
Databases
CATH, GenBank, GeneCensus, ModBase, PDB, Presage, SWISS-PROT+TrEMBL
Template Search
123D, BLAST, DALI, FastA, Matchmaker, PHD, PROFIT, Threader, UCLA-DOE
FRSVR
Sequence Alignment BCM Server, BLAST, Block Maker, CLUSTAL, FASTA3, Multalin
Modeling
Coposer, Congen, CPH Models, Dragon, ICM, InsightII, Modeller, Look,
Quanta, Sybyl, Scwrl, Seisss-Mod, What If
Verification
Anolea, Aqua, Biotech, Errat, Procheck, ProCeryon, Prosall, PROVE, SQUID,
VERIFY3D, WHATCHECK
Visualization
CHIMERA, SWISS-PDBViewer, RasMol, Pymol
Academic
SLAM III
Commercial
Extend, Crystal Ball, MedModel, ProModel, Simul8, Micro Saint, ACSL, Arena,
GPSS/H, iThink, MAST, MODSIM III, Simprocess, Taylor II
In considering the tools in
Table 9-2
, it's important to consider that most of these are in
flux—especially those developed for bioinformatics-specific roles. New releases of existing systems
and new programs that replace current programs are a constant occurrence. In contrast, the
commercial, general-purpose programs are more stable, in part because of demand from a variety of
arenas that don't include bioinformatics. Of course, as discussed previously in the section on
fundamentals, it's imperative to understand the assumptions made by the simulation system
designer and then to decide if those assumptions are in agreement with your needs.
