Computational Science & Bioinformatics Lab                                                                   Software and Hardware Description

I. Hardware:

SGI O2 Server: IRIX 6.5.17 

DELL Workstation: Linux Enterprise WS 3.0

P4 Windows 2003 Print server 

22 PC’s, Dell - GX260/240: Windows XP

hp 4200n LaserJet Printer

hp 2600d InkJet Color Printer

hp ScanJet Scanner

EPSON Expression 1680 X-ray Film Scanner

II. Software

1- Structural Biology

Insight II: Complete life science molecular modeling environment. Central graphical interface to expert-level modeling packages.

Discover: A molecular mechanics simulation environment offering energy minimization, dynamics and Monte Carlo techniques for life science applications.

DeCipher: Tools for static and dynamic structural analysis.

CFF: A Class II force field derived within a consistent quantum mechanical framework, including anharmonicity and cross terms. Optimized to describe common organic and biomolecular chemical functional groups.

Biopolymer: A general suite of tools for protein and peptide design, modification, and analysis. Requires Insight II. CHARMm or Discover, and Profiles-3D strongly recommended.

Homology: A suite of tools for comparative model building of proteins, including sequence and structure alignment tools, structure and loop generation/refinement, and analysis.

Modeler: Provides automated homology modeling. Requires Insight II.

Profiles-3D: A 3D protein structure environment analysis package for sequence-to-sequence comparisons. Requires Insight II.

SeqFold: A fold recognition package for sequence-to-structure comparisons. Requires Insight II.

Affinity: An energy-based automated ligand-protein docking module using implicit solvent terms. Requires Insight II and Discover.

DelPhi: A validated set of tools to compute the Poisson-Boltzmann electrostatic potentials of molecular systems, including modification of ionic strength, dielectric constants, and boundary conditions. 

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