CLICK – Comparison of Biomolecular 3D Structures

CLICK

:: DESCRIPTION

CLICK is capable of superimposing the 3D structures of biomolecules, the Cartesian coordinates of whose constituent atoms are presented in the PDB format. In addition to coordinates, the web server can make use of similarity of other structural features such as secondary structure, solvent accessible surface area, and residue depth to guide the alignment. CLICK first looks for cliques of points (3–7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants.

CLICK Online Version

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLICK

:: MORE INFORMATION

Citation:

Nguyen,M.N., Tan,K.P., and Madhusudhan,M.S. (2011)
CLICK – Topology independent comparison of biomolecular 3D structures.
Nucleic Acids Res., doi:10.1093/nar/gkr393

MolScript 2.1.2 – Display Molecular 3D Structures

MolScript 2.1.2

:: DESCRIPTION

MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.The user supplies an input file (the script) which specifies the coordinate file, what objects to render and the exact appearance of the objects through the graphics state parameters.

::DEVELOPER

Per Kraulis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • SGI IRIX / Linux

:: DOWNLOAD

 MolScript

:: MORE INFORMATION

Citation

P. J. Kraulis,
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Journal of Applied Crystallography (1991) v 24, pp 946-950.

Protein Explorer 2.80 – Visualize 3D Structures of Macromolecules

Protein Explorer 2.80

:: DESCRIPTION

Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind.

::DEVELOPER

Eric Martz , the University of Massachusetts

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac

:: DOWNLOAD

Protein Explorer

:: MORE INFORMATION

Citation

Martz E.
Protein Explorer: easy yet powerful macromolecular visualization.
Trends Biochem Sci. 2002 Feb;27(2):107-9.