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338 Database entries



WebMol


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OS: Java

License: Freeware, Registration





WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application. Graphical features include:

wireframe representation of structures with full atomic detail
different color coding schemes
atom type
secondary structure
B-factor
chain
burial state
sequence conservation according to HSSP
side-by-side stereo view with adjustable separation of the images
mouse driven zoom, translate and drawing slab manipulations
selecting focus; i.e. setting point of rotation to a desired position
selecting residues according to type or burial state and regions within proteins
animations of rocking motions with adjustable angular range
variable background colors

Tools

distance, angle, dihedral angle measurements
detection of steric conflicts
peptide bond planarity analysis
interactive distance matrix plot and other 2D-projection plots
interactive Ramachandran plot
dot surface
numerical calculation of solvent accessible, van der Waals surface area, and volume
detection of cavities
axes assignments for secondary structural elements
secondary structural element packing analysis
hydrophobic moment vectors of secodary structural elements
mainchain-mainchain hydrogen bond detection

Input options

URL, ftp, file, text string
Format: PDB

Output options:
Postscript

http://www.cmpharm.ucsf.edu/~walther/webmol.html



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