IU MolViz Application Guide
The MolViz Application Guide pertains to topics, molecular modeling
applications, and UNIX applications specific to the computing environment
of the Molecular Visualization Facility of the Department of Chemistry
at Indiana University.
If you have questions or suggestions regarding these notes, contact the MolViz Facility Staff.
|Visualizing 3D molecular structures
JaMM, Swiss-PdbViewer, Mercury,
|Classical Mechanical Calculations
|Quantum Mechanical Calculations
|Systematic Conformational Searches
|Calculation of Geometrical Properties
|Docking a small molecule and a large molecule
|Docking two large molecules
||not yet available
|Calculating the Electrostatic Field of a Macromolecule
|Sequence Alignment and Model-Building
|X-Ray Crystallography Applications
|NMR Spectroscopy Applications
Molecular Modeling Application List
(IN ALPHABETICAL ORDER)
- Takes a multiple sequence alignment in AMPS block-file
format and a set of formatting commands and produces a PostScript file
that contains a sequence alignment figure suitable for publication.
- A suite of programs designed for multiple alignment of protein sequences
and flexible pattern matching.
- A Monte-Carlo computer simulation method for automated docking of flexible
ligands to receptors. This non-graphical program has been augmented with scripts and notes
for interfacing AutoDock results with InsightII.
- A program for translating one type of molecular structure file format to
another file format.
- Cambridge Structural Database
- The CSD is the largest searchable database of experimentally determined
crystal structures. This system includes graphical search, retrieval and
data visualization software.
- A comprehensive molecular modeling system. The suite of Cerius2
programs supported by the IU MolViz Facility is focused particularly for
materials science modeling.
- The Crystallography & NMR System for calculation of biomolecular structure
models from crystallographic or NMR experimental results.
- Calculates the electrostatic field generated by a molecule via the Poisson-Boltzmann
- Flexible ligand docking using a genetic algorithm.
- A general-purpose Ab initio molecular orbital package. This application
is designed to model a broad range of molecular systems under a variety
of conditions, performing its computations starting from the basic laws
of quantum mechanics.
- A system for scanning one-dimensional gels, displaying lane profiles, and
calculating areas under the peaks.
- GMMX is now built into PC-MODEL v7.0 and later versions. However, the original
GMMX v1.0 program is retained here for backwards-compatibility.
- A molecular graphics toolbox for the display of molecules and their properties and
the analysis of molecular structures and dynamics trajectories (originally as the graphics interface for
the OpenMol set of programs).
- A hydrogen bond calculation program.
- Insight II
- A comprehensive molecular modeling system. The suite of Insight II programs
supported by the IU MolViz Facility is focused particularly for bio-pharmaceutical
modeling. Additional scripts are included for extra functionality.
- A locally written Java applet for examining molecular structures.
- A crystal structure visualizer developed by CCDC.
- A graphical pre- and post-processing package for displaying molecular and
electronic structure from the Ab Initio packages GAMESS-UK, GAMESS-US and
GAUSSIAN and the Semi-Empirical packages Mopac/Ampac.
- A molecular graphics program for displaying molecular and electronic
structure data from electronic structure programs, such as GAUSSIAN 9x, ADF,
- A molecular graphics program for displaying, analyzing, and manipulating
the three-dimensional structure of biological macromolecules, with special
emphasis on the study of protein or DNA structures determined by NMR.
- A program for creating schematic or detailed molecular graphic images from molecular
3D coordinates (PDB files), usually, but not exclusively, protein structures.
- A general-purpose semi-empirical molecular orbital package for the study
of chemical structures and reactions. Additional notes and scripts are
included for interfacing the input and output files of this non-graphical
program with other programs.
- Calculates the atomic accessible surface defined by rolling a probe of
given size around a van der Waals surface.
- A Macromolecular Crystallography Package.
- A complete molecular modeling package, especially for small molecules.
One of the most user-friendly programs available. Draw structures, minimize
structures, search for different conformations of structures, and dock
two or more structures.
- Programs for assessing the overall geometrical quality of protein structures,
for analyzing NMR ensembles, and for comparing related protein structures
- A molecular graphics program intended for the visualization of proteins,
nucleic acids and small molecules. The program is aimed at display, teaching
and generation of publication quality images.
- Interactively displays molecular models, creates publication quality images,
and analyzes crystallographic results. Particularly intended for protein
and nucleic acid models.
- Given a set of protein domains with a similar structure, one can use STAMP
to produce a multiple alignment and associated superimposition based on
a comparison of 3D structures.
- A molecular graphics program for viewing and manipulating PDB files.
- A molecular visualization program for displaying, animating, and analyzing large
biomolecular systems using 3-D graphics and built-in scripting.
- XMView is a locally written Unix (& Linux) application which generate publication quality molecular
graphics. CMView is the CAVE
application that can be used in conjunction with XMView.
- This application uses interactive computer graphics to introduce basic
concepts of X-ray diffraction by crystals.
- A package for molecular simulations, particularly for reduced representation
models. There are several methods for Energy Minimization, Molecular Dynamics
and Monte Carlo simulations.
UNIX Application Notes
- IU Knowledge Base
- A highly-recommended searchable database of Computer Support Information,
specifically oriented toward capabilities at Indiana University, but generally
useful to others as well.
Other Notes and Topics
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Last updated: 6/6/2002