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Molecular Modeling

Protein Structural Prediction

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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.

[more info][13639]

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Garlic Software
[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.

[more info][12354]

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GRASP Software
[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.”

[more info][12348]

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[Molecular Software] Molecular visualization software with an easy to use GUI.

[more info][12345]

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JOY Software
[University of Cambridge] JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features.

[more info][12310]

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[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.

[more info][11305]

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LigBuilder v1.0 Software
[Institute of Physical Chemistry, Peking University] LigBuilder is a multi-purpose program written for structure-based drug design. Based on the 3D structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them.

[more info][12169]

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[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.”

[more info][12352]

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Molecular Structure Computer Programs
[University of Lunds] Several program packages dealing with molecular structure analysis and NMR data analysis.

[more info][12299]

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This is a program for the analysis and display of molecules.

[more info][11315]

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MolPOV Software
[University of Florida] “A PDB to POV file converter and molecular visualization tool for MS Windows.”

[more info][12347]

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MolScript Software
[Avatar Software AB] “MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.”

[more info][12344]

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[S. Hubbard & J. Thornton, UMIST] A stand alone program that calculates the accessible area of a molecule from a PDB format file. It can calculate the atomic and residual accessiblities for both proteins and nucleic acids.

[more info][11114]

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[Univ. College London] Analyzes a protein coordinate file and provides details of the structural motifs in the protein.

[more info][11273]

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[University College London] “Promotif analyzes a protein coordinate file and provides details of the structural motifs in the protein.”

[more info][12302]

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Protein Analysis & Modelling Software
[University College London] Publicly available bioinformatics software. Most of these programs are for the analysis of protein sequence and structure.

[more info][12301]

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[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.

[more info][11338]

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STING Server and Software
[Weizmann Institute] “STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING’s Graphics Frame) and sequence (in STING’s Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis.”

[more info][12342]

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VMD Software
[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.”

[more info][12350]

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[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. ”

[more info][12358]

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YASARA Software
[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.”

[more info][12351]