1,330
edits
Model Evaluation: Difference between revisions
more details for ligplot according to ccp4bb posts
No edit summary |
(more details for ligplot according to ccp4bb posts) |
||
| (2 intermediate revisions by one other user not shown) | |||
| Line 4: | Line 4: | ||
* [http://www.sdsc.edu/CCMS/FP/index.html FADE and PADRE ]- Shape and Complementarity Server | * [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://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.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 | * [http://www.ccp4.ac.uk/dist/html/ncont.html NCONT ] - (ccp4) analyses contacts between subsets of atoms in a PDB file | ||
* [http://www.biochem.ucl.ac.uk/bsm/PP/server/ Protein-Protein Interaction Server] - stats on your chain interfaces and to obtain surface calculations | * [http://www.biochem.ucl.ac.uk/bsm/PP/server/ Protein-Protein Interaction Server] - stats on your chain interfaces and to obtain surface calculations | ||
* [http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - anisotropic displacement parameters statistics | * [http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - anisotropic displacement parameters statistics | ||
* [http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html | * [http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html SURFACE and AREAIMOL] - (ccp4) -surface programs | ||
* [http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html VOIDOO] - look for interior cavities | * [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) | * [http://redpoll.pharmacy.ualberta.ca/vadar/ VADAR ] - (Volume, Area, Dihedral Angle Reporter) | ||