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Molecular Science Computing Facility- Other Application Software at MSCF
Life Sciences Software - Insight II 97.0
Insight provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. The MSCF has the selected Insight modules listed below. To access this software, please contact the MSCF Scientific Consultants by sending e-mail to mscf-consulting@emsl.pnl.gov.
Discover | Analysis | Biopolymer | Homology | DelPhi | DMol | Turbomole
- Insight II - Home Page
- The home page for Accelrys' Insight II. Gives descriptions of all their modules.
Discover
Molecular mechanics/dynamics
The FDiscover (the FORTRAN version of Discover®) performs energy minimization, template forcing, torsion forcing, and dynamic trajectories and calculates peroperties such as interaction energies, derivatives, mean square displacements. It provides tools for performing simulations under various conditions including constant temperature, constant pressure, constant stress, periodic boundaries, and fixed and restrained atoms.
Analysis
Analyzing molecular dynamics trajectories
The Analysis module is used to display data, especially from molecular conformation analyses, in graphs or molecular animation. Typically, the input data of molecular conformations comes from the Discover program, but this data can come from any source, provided it is formatted in a way that is recognizable to the Insight II program.
Biopolymer
Building macromolecules
The Biopolymer module facilitates the building and modification of peptides, proteins, polysaccharides and nucleic acids. In particular these commands can be used to:
- Build up peptide sequences while imposing secondary structure; delete and replace residues.
- Build and modify molecular models of nucleic acid compounds.
- Construct polysaccharides, alter or change an existing monosaccharide in a polysaccharide and join polysaccharides together.
- Predict the backbone conformation of a protein from its alpha-carbon trace.
- Search for the optimal division of the protein structure into a set of separated domains.
Homology
Making 3D protein models from sequences
Homology is a computer program package that helps you build the structure of a protein when you know only its amino acid sequence and the complete atomic structure of at least one other reference protein.
DelPhi
Electrostatic potential in and around molecules
DelPhi is a software package that calculates the electrostatic potential in and around macromolecules, using a finite difference solution to the nonlinear Poisson-Boltzmann equation. The program allows specification of ionic strength as well as dielectric constants of both the solvent and the molecule of interest.
DMol
Density functional ab-initio code
DMol is a first-principles (ab initio) quantum chemistry software package that performs accurate theoretical calculations on a wide range of compounds, including metal clusters, biological compounds, organometallics, and organic compounds.
Turbomole
Ab-initio code
Turbomole is a general-purpose, ab initio quantum chemistry program package designed for the prediction of molecular energies, structures, spectra, reactivity, and properties.