Modelling Tools


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 Cn3D is NCBI's 3D structure viewer. Cn3D is a visualization tool for biomolecular structures, sequences, and sequence alignments. What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application.

Last Updated on Tuesday, 02 November 2010 00:11


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KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research. KiNG builds on Mage, JavaMage, and the "kinemage" (kinetic image) concept to deliver a full-featured Java application with a user-friendly interface and integrated editing features. It also operates as a Java applet to promote easy access to kinemages from a web browser.





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Dang reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base. In its most basic form, it writes out dihedral angles (phi, psi, chi) hence the name. The output is formated for easy parsing by awk, grep, sort and other UNIX utilities.


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YASARA View is available for free and contains all the functions you need to explore a macromolecular structure interactively. As a bonus, you get YASARA's innovative 3D engine, which is up to 35 times faster than what you usually know from OpenGL (see benchmarks ), you can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins. Included is YASARA Movie, a player for multimedia presentations and tutorials created with any of the higher stages.


Last Updated on Monday, 01 November 2010 23:59

VMD Visual Molecular Dynamics

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VMD designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.



Last Updated on Tuesday, 01 March 2011 11:10

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