Scientific Software Applications

The Research Computing group offers a wide variety of scientific software applications and tools for researchers on campus. These software applications are available for many of the Research Computing servers. Selecting any of the applications below will lead you to a listing of the information provided by the Research Computing group about that application, including documentation, FAQs, location of manuals, links to other resources, and more.

The instructions given to run these programs assume a familiarity with the Research Computing infrastructure and the UNIX, Linux, Microsoft Windows, or MacOS operating systems, as appropriate.

Table 1. Available Scientific Software

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).
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.

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.

Materials Studio Materials Studio is a computational package for researchers who need to perform expert-level modeling and simulation tasks in a powerful environment. Materials Studio contains tools useful for applications in Crystallization, Polymers and Classical Simulations, Quantum Mechanics and Catalysis, and Statistics.
Mogul Mogul is contained as part of the Cambridge Structural Database.
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).
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.
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.

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