Software Title

Software Description

Amber

The Assisted Model Building with Energy Refinement (Amber) is a general-purpose molecular mechanics and dynamics program designed for the refinement of macro-molecular conformations using an analytical potential energy function.

Babel

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling and computational chemistry. It is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

BLAST

BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs for exploring all of the available sequence databases regardless of whether the query is protein or DNA. These well-known applications are written and maintained by the National Center for Biotechnology Information (NCBI).

Cerius2

Cerius2 provides a user-friendly and easy-to-use molecular simulation and modeling environment. It offers a wide range of scientific application modules for various molecular environments including both Materials Science and Life Science.

Note: You must be a "tcsh" or "csh" user to benefit from the full functionality of this package.

Cambridge Structural Database (CSD)

Cambridge Structural Database (CSD) contains the largest database of experimentally determined organic and organometallic crystal structures in the world. The database comes with a suite of graphical search, retrieval, data manipulation, and visualization software.

Note: You must be a "tcsh" or "csh" user to benefit from the full functionality of this package.

CNSsolve

CNSsolve is a flexible multi-level hierarchical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

CPMD

The CPMD (Car-Parrinello Molecular Dynamics) code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. CPMD runs on many different computer architectures and it is well parallelized (MPI and Mixed MPI/SMP).

Felix

Felix is no longer being offered by the Research Computing group.

Fluent

Fluent is no longer being offered by the Research Computing group.

GAMESS

The General Atomic and Molecular Electronic Structure System (GAMESS) is a parallel (via MPI) ab-initio quantum chemistry package.

Gaussian

Gaussian is capable of predicting many properties of molecules and reactions, Including molecular energies and structures, bond and reaction energies, spectroscopic (IR, UV, Raman, NMR) properties, reaction pathways.

GROMACS

GROMACS is a versatile package for performing molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Discovery Studio

Discovery Studio is a single unified, easy-to-use, graphical interface for powerful drug design and protein modeling research. Discovery Studio contains both established gold-standard applications (e.g., Catalyst, MODELER, CHARMm, etc.) with years of proven published results, as well as and cutting-edge science to address today’s drug discovery challenges.

Note: You must be a "tcsh" or "csh" user to benefit from the full functionality of this package.

Mogul

Mogul is contained as part of the Cambridge Structural Database.

MolPro

Molpro is a complete system of ab-initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors.

NBO

NBO is supplementary software to perform natural bond orbital analysis. Natural Bond Orbitals (NBOs) are localized few-center orbitals that describe the Lewis-like molecular bonding pattern of electron pairs. This package can also be applied to obtain localized molecular orbitals, to perform steric analysis, population analysis, dipole moment analysis, chemical shielding analysis, resonance theory analysis, etc.

NWChem

NWChem is a computational chemistry package developed by the Molecular Sciences Software group of the Theory, Modeling & Simulation program of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL).

O

O is a general purpose macromolecular modeling environment. The program is aimed at scientists with a need to model, build and display macromolecules. Unlike other molecular modeling programs, O is a graphical display program built on top of a versatile database system.

Pise

Pise is a web interface to UNIX programs for scientific applications. Most scientific applications are written for UNIX platforms but most scientists who run those applications do not wish to use a UNIX platform to run them. Catherine Letondal (letondal@pasteur.fr) from Pasteur Institute created this web interface to run scientific applications in a web form environment, thus eliminating the difficulties associated with the learning of parameter syntax and semantics in UNIX job submissions.

PyMOL

PyMOL is a molecular viewer, render tool, 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and carbohydrates, as well as small molecule structures of drug leads, inhibitors, metabolites, sugars, nucleoside phosphates, and other ligands including inorganic salts and solvent molecules.

QUANTA

QUANTA is a program for displaying and manipulating molecular structures. It also includes a front end for the CHARMM molecular mechanics/dynamics package.

Note: You must be a "tcsh" or "csh" user to benefit from the full functionality of this package.

Schrodinger

Schrodinger is a suite of computational chemistry and molecular modelling packages which include quantum mechanics calculations, reaction path calculations through QM/MM, and protein structure prediction. Schrodinger also contains various packages useful for pharmaceutical research, such as ligand-receptor docking, binding affinity prediction and other structure-based drug design modules. Finally, Schrodinger contains the Maestro program which provides a graphical user interface to all Schrodinger programs.

SOLAR

SOLAR is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions.

Sybyl

Sybyl provides the front end for comprehensive tools for molecular modeling such as structure building, optimization, visualization of structures and associated data. Additional modules of Sybyl can be added to the base Sybyl to enhance its capability.

Note. You must be a "tcsh" or "csh" user to benefit from the full functionality of this package.