Model Evaluation: Difference between revisions

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* [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] - Calculate electrostatic potential

* [http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html LIGPLOT] - Interactions around a ligand of piece of structure

* [http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html LIGPLOT] - Interactions around a ligand of piece of structure. There is also LigPlot+ at http://www.ebi.ac.uk/thornton-srv/software/LigPlus/; the [http://www.ebi.ac.uk/pdbsum/ PDBsum] server internally runs ligplot and returns pdf files; non-released PDB files can be handled using the "generate" option in the left panel

* [http://www.bioinf.manchester.ac.uk/naccess/ NACCESS] - Surface area calculaitons, per residue, or atom

* [http://www.ccp4.ac.uk/dist/html/ncont.html NCONT ] - (ccp4) analyses contacts between subsets of atoms in a PDB file

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* [http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html VOIDOO] - look for interior cavities

* [http://redpoll.pharmacy.ualberta.ca/vadar/ 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.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] - Calculate electrostatic potential
-* [http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html LIGPLOT] - Interactions around a ligand of piece of structure
+* [http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html LIGPLOT] - Interactions around a ligand of piece of structure. There is also LigPlot+ at http://www.ebi.ac.uk/thornton-srv/software/LigPlus/; the [http://www.ebi.ac.uk/pdbsum/ PDBsum] server internally runs ligplot and returns pdf files; non-released PDB files can be handled using the "generate" option in the left panel
 * [http://www.bioinf.manchester.ac.uk/naccess/ NACCESS] - Surface area calculaitons, per residue, or atom
 * [http://www.ccp4.ac.uk/dist/html/ncont.html NCONT ] - (ccp4) analyses contacts between subsets of atoms in a PDB file
@@ Line 12: / Line 12: @@
 * [http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html VOIDOO] - look for interior cavities
 * [http://redpoll.pharmacy.ualberta.ca/vadar/ VADAR ] - (Volume, Area, Dihedral Angle Reporter)
-STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:inaccessible cavities