Bioinformatics

Investigators using INBRE facilities, services or resources are required to cite NIH Grant Number P20 RR-016464 from the INBRE Program of the National Center for Research Resources in all publications and presentations. © Nevada INBRE 2006.

Other Molecular Modeling Resources

General molecular modeling software

QUANTA (Accelrys), a 2D and 3D modeling environment for molecules designed to aid crystallographic structure solution. It is much like Sybyl or InsightII. This package is no longer supported and is provided on an “as is” basis.

General molecular mechanics and molecular dynamics software

CHARMM (Harvard)
AMBER (UCSF)
NAMD (UIUC)
ESP (UH)
TINKER (WUSTL)
GROMACS (Max Planck Institute)
NWCHEM (PNNL)

These packages provide command-line access to powerful methods of calculating the energies and dynamics of chemical systems. Commercial versions of these program are at the heart of the graphical modeling environments mentioned above.

Poisson-Boltzman electrostatics and Brownian dynamics

GRASP/Delphi (Columbia)
UHBD (UCSD/UH)

These packages allow for the determination of electrostatic potentials and energies, solvation energies, and related quantities like pKa’s.

Ligand interactions, docking, and quaternary structure prediction

HEX (Aberdeen)
ZDOCK (BU)
DOCK (UCSF)
AUTODOCK (Scripps)
Modeller (UCSF)
RAPTOR (Bioinformatics Solutions)
Rosetta (U. Washington)

These packages allow for the prediction of molecular structures and molecular interactions.

Quantum mechanical and mixed quantum/classical chemistry software:

NWChem (PNNL)
GAMESS (Iowa St.)
MolPro (Cardiff)

These packages allow for determination of molecular properties that are more dependent on a more precise understanding of the sub-atomic structures of molecules.

High-Performance Computing:

The bulk of these packages are also parallelized to run across multiples computers at once, allowing the power of existing and future servers to be leveraged in order to scale to the computational demands of the facility's users.