Bioinformatics & Genomics
Molecular Modeling & Visualization
Programs Integrated with Web Sites
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B Molecular Modeling
[Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics.
Center for Advanced Research in Biotechnology
[University of Maryland and the National Institute of Standards and Technology] Joint government/university research site. Includes research and graduate study opportunities, a biological macromolecular crystallization database, and TkRaster3D.
Cornell Theory Center
[Advance Cluster Computing Consortium] A high-performance computing and interdisciplinary research center. This site provides information about the center, resources like software and training, and research information.
[UCSF] DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together.
[University of Split, Croatia] A free molecular visualization program intended to ease some of the hardships non-computer scientists may have with RasMol's command line interface.
[Columbia University] "GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties."
Source of HyperChem, which "is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use." It unites 3-D visualization and animation with quantum chemical
calculations, molecular mechanics, and dynamics. An extension product, Q-Chem, adds quantum chemistry methods.
[Molecular Software] Molecular visualization software with an easy to use GUI.
[D. Richardson, Duke Univ.] A package of 2 programs, Prekins and Mage, that enables the user to create a 3-D image from a PDB-format coordinate file, which then can be modified.
[San Diego Supercomputing Center] "The MICE application provides high quality, interactive visualization of molecular scenes. Written in JavaTM and Java3D, MICE is designed according to the Java philosophy of “write once, run anywhere.” Portable and web-deliverable, the MICE application enables users to not only view molecular scenes on their own computer, but to distribute these scenes and interact with other users anywhere on the internet."
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This is a program for the analysis and display of molecules.
[University of Florida] "A PDB to POV file converter and molecular visualization tool for MS Windows."
[Avatar Software AB] "MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations."
Noncovalent Bond Finder
[University of Massachusetts] [Annotation pending]
Raster3D Version 2.5
[University of Washington] Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program
renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. Raster3D can also be used to render pictures composed in other programs such
as Molscript in glorious 3D with highlights, shadowing, etc.
[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.
[Drug Design Laboratory, Milan University] VEGA was developed to create a bridge between most of the molecular software
packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. Also implemented are some features that are useful to analyze, display
and manage the 3D structures of molecules. Features include: atomic charge attribution, force field attribution, calculation of molecular surfaces, calculation of ligand-receptor interaction energy, evaluation of logP and lipole, dynamic trajectory analysis, and molecule solvatation.
[University of Illinois at Urbana-Champaign] Visual Molecular Display "is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code."
[San Diego Supercomputing Center] "The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1, Windows95, and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above. "
[University of Graz] "YASARA is an interactive real-time molecular dynamics program, covering various topics in the field of molecular modeling, protein fold calculation (based on NMR data), tertiary structure prediction, protein / DNA docking, and parallel macromolecular dynamics."
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