Software on Zeus

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Software on Zeus


Gaussian

Performs quantum mechanical electronic structure calculations on molecular systems. One of the most widely used software packages by North Carolina researchers and educators. ECU has a statewide license for Gaussian.

Accelrys

Consists of a suite of programs for doing calculations in Life and Material Sciences. ECU has 49 license tokens for the Accelrys products. We have the Materials Studio product suite which includes:

DMol3: A unique density functional theory (DFT) quantum mechanical code that allows users to study problems in the chemical and pharmaceutical industry and in materials science with high accuracy and reliability. DMol3 can simulate processes in gas phase, solvent, surface, and solid environments. As such, it is well suited to research problems in chemistry, materials science, chemical engineering, and solid state physics.

Cerius2: A graphical interface for a molecular simulation and modeling environment for the Material Sciences. ECU has the following modules for Cerius2:

Amorphous Builder: Builds amorphous molecular structures, which can be represented in the molten state, in solution, or in the semicrystalline state.

Autoludi: Uses the existing Accelyrs Ludi program for denovo drug design.

Castep: Simulates electronic relaxation to ground state for metals, insulators, or semiconductors.

Compass: First ab initio forcefield that enables accurate, simultaneous prediction of structural, conformational, vibrational and thermophysical properties for a broad range of molecules in isolation and condensed phases.

Crystal Builder: Provides a robust and versatile crystal builder and editor. Also includes plane and facet tools to aid in visualization of crystal structures.

Discover: Performs energy minimization, template forcing, torsion forcing, and dynamic trajectories and calculates properties such as interaction energies, derivatives, mean square displacements and vibrational frequencies.

Ludi: Assists in the design of new and selective ligands for proteins (e.g., enzyme inhibitors), one of the most important applications in contemporary rational drug design.

Minimizer: Minimizes the structure of periodic and nonperiodic systems.

Open Force Field: Foundation module required for many molecular mechanics energy calculations performed in Cerius2.

QSAR

Can be used to generate and analyze structure-activity relationships of potential lead compounds and to visualize and analyze receptor-pharmacophore interaction patterns.

Used for constructing 2D-periodic structures by cleaving a plane from a crystal or by placing atoms and fragments within a suitable 2D-surface cell.

InsightII

Graphical interface for a molecular simulation and modeling environment for the Life Sciences. ECU has the following modules for Cerius2:

Affinity: A suite of programs for automatically docking a ligand (guest) to a receptor (host).

Binding Site Analysis: Used for identifying and characterizing protein active sites, binding sites, and functional residues from protein structures and multiple sequence alignments.

Biopolymer: FacilitateS the building and modification of peptides, proteins, polysaccharides and nucleic acids.

CFF: This is a class II forcefield for molecular simulations.

Decipher: Allows users to abstract molecular properties dynamically from molecular structures and simulations.

Delphi: Calculates the electrostatic potential in and around macromolecules, using a finite difference solution to the nonlinear Poisson-Boltzmann equation (see for a review Honig et al. 1993).

Discover/Discover3: It performs energy minimization, template forcing, torsion forcing, and dynamic trajectories and calculates properties such as interaction energies, derivatives, mean square displacements, and vibrational frequencies. It provides tools for performing simulations under various conditions including constant temperature, constant pressure, constant stress, periodic boundaries, and fixed and restrained atoms.

Homology: It 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.

Ludi: Assists in the design of new and selective ligands for proteins (e.g., enzyme inhibitors), one of the most important applications in contemporary rational drug design.

Modeler: It is an automated homology modeling scheme designed to find the most probable three dimensional structure of a protein, given its amino acid sequence and its alignment with related structures. It derives 3D protein models without the time consuming separate stages of core region identification and loop region building or searching that are inherent to manual homology modeling schemes.

Profiles 3D: It address the question: given a three-dimensional protein structure, what amino acid sequences are compatible with that structure?

Search/Compare: It enables one to calculate and operate on molecular volumes, to superimpose two or more molecules, to search systematically for the sterically allowed conformations of a molecule, and to quickly find and examine conformations of interest after they have been generated.

Sketcher: Allows one to sketch a molecule and then convert it to a reasonable 3D structure

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