Tag: Biomolecular

Adun 0.81 – Biomolecular Simulator

Adun 0.81

:: DESCRIPTION

Adun is a free  multipurpose high performance production molecular simulator.The Adun molecular simulation application has been designed from the ground up to cater for a broad range of users and needs, from computational chemists to experimental biologists.

::DEVELOPER

the Computational Biochemistry and Biophysics Lab at GRIB-IMIM/UPF

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOSX

:: DOWNLOAD

 Adun

:: MORE INFORMATION

Citation

M. A. Johnston, I. F. Galván, and J. Villà-Freixa,
“Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.,”
J Comput Chem, vol. 26, iss. 15, pp. 1647-1659, 2005.

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