Gaussian

The Gaussian software package performs quantum mechanical electronic structure calculations on molecular systems. It is one of the most versitle and widely used software packages by North Carolina researchers and educators. ECU has a statwide license for Gaussian.

NwChem

The NwChem software package performs quantum mechanical electronic structure calculations on molecular systems. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.

GAMESS

The GAMESS software package performs quantum mechanical electronic structure calculations on molecular systems.

MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny

POY

POY is a program for phylogenetic analysis of DNA and other data using dynamic homology

Amber

The Amber software package is a suite of programs for performing and analysing molecular dynamic simulations on biomolecules.

Accelrys

The Accelrys software package consists of a suite of programs for doing calculations in the Life and Material Scineces. ECU has 49 token licenses for the Accelrys products. Most of the Accelrys application software is installed on the SGI Origin 350.

• SeqWeb
  • SeqWeb is a web-based user interface to the Accelrys GCG sequence analysis software.

• Materials Studio
  • Materials Studio is a comprehensive suite of modeling and simulation solutions for studying chemicals and materials, including crystal structure and crystallization processes, polymer properties, catalysis, and structure-activity relationships.
    • 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.
    • Amorphous Cell: A versatile technique used to develop an understanding of molecular properties and behavior, especially for liquids and amorphous polymers.
    • Castep: It is capable of simulating electronic relaxation to ground state for metals, insulators, or semiconductors.
    • Compass: The first ab initio forcefield that has been parameterized and validated using condensed-phase properties in addition to various ab initio and empirical data for molecules in isolation
    • Discover: is an atomistic simulation program for the study of molecular systems and materials.
  
  
• Discover Studio
  • Discover Studio is a comprehensive suite of modeling and simulation solutions for protein modeling and computational chemistry
    • Biopolymer: It facilitate the building and modification of peptides, proteins, polysaccharides and nucleic acids.
    • Charmm_Lite: is an atomistic simulation program for the study of molecular systems
    • Charmm: Dock ligands accurately with the CDOCKER protocol. Refine the results of your docking experiment by performing CHARMm in situ ligand minimization with optional receptor atoms included. Score docked poses using the physics-based Molecular Mechanics-Poisson Boltzmann with Surface Area (MM-PBSA) and Molecular Mechanics-Generalized Born with Surface Area (MM-GBSA) and Linear Interaction Energy (LIE) methods.
    • Autoludi: It uses the existing Accelyrs Ludi program for de novo 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.
    • Many more modules:
  
  
• Cerius2
  • Cerius2 is a graphical interface for a a molecular simulation and modeling environment for the Material Sciences. ECU has the following modules for Cerius2:
    • Amorphous Builder: It builds amorphous molecular structures, which can be represented in the molten state, in solution, or in the semicrystalline state.
    • Autoludi: It uses the existing Accelyrs Ludi program for de novo drug design.
    • Castep: It is capable of simulating electronic relaxation to ground state for metals, insulators, or semiconductors.
    • Compass: It is the first ab initio forcefield that enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases.
    • Crystal Builder: provides a robust and versatile crystal builder and editor. It also includes plane and facet tools to aid in visualization of crystal structures.
    • Discover: 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.
    • 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 periodic and nonperiodic systems.
    • Open Force Field: It is the foundation module required for many molecular mechanics energy calculations performed in Cerius2.
    • QSAR: It can be used to generate and analyze structure-activity relationships of potential lead compounds and to visualize and analyze receptor-pharmacophore interaction patterns.
    • Surface Builder: It is 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
  • InsightII is a graphical interface for a a molecular simulation and modeling environment for the Life Sciences. ECU has the following modules for Cerius2:
    • Affinity: It is a suite of programs for automatically docking a ligand (guest) to a receptor (host).
    • Binding Site Analysis: It is used for dentifying and characterizing protein active sites, binding sites, and functional residues from protein structures and multiple sequence alignments.
    • Biopolymer: It facilitate the building and modification of peptides, proteins, polysaccharides and nucleic acids.
    • CFF: This is a class II forcefield for molecular simulations.
    • Decipher: It allows users to abstract molecular properties dynamically from molecular structures and simulations.
    • Delphi: It 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.