Model Evaluation: Difference between revisions

Revision as of 10:07, 7 March 2008

sfcheck - run CCP4Online sfcheck
CASTp - webserver for identification and measurements of surface accessible pockets as well as interior
DIMPLOT - Interactions between monomers of a dimer
FADE and PADRE - Shape and Complementarity Server
GRASP - Calculate electrostatic potential
LIGPLOT - Interactions around a ligand of piece of structure
NACCESS - Surface area calculaitons, per residue, or atom
NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file
Protein-Protein Interaction Server - stats on your chain interfaces and to obtain surface calculations
PARVATI - anisotropic displacement parameters statistics
[1] - SURFACE and AREAIMOL (ccp4) -surface programs
VOIDOO - look for interior cavities
VADAR - (Volume, Area, Dihedral Angle Reporter)

STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:inaccessible cavities

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 * [http://www.biochem.ucl.ac.uk/bsm/ligplot/manual/man8.html DIMPLOT ]- Interactions between monomers of a dimer
 * [http://www.sdsc.edu/CCMS/FP/index.html FADE and PADRE ]- Shape and Complementarity Server
-* [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP GRASP]
+* [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP GRASP] - Calculate electrostatic potential
 * [http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html LIGPLOT] - Interactions around a ligand of piece of structure
 * [http://www.bioinf.manchester.ac.uk/naccess/ NACCESS] - Surface area calculaitons, per residue, or atom