Model Evaluation: Difference between revisions
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(more details for ligplot according to ccp4bb posts) |
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* [http://www.ccp4.ac.uk/dist/html/sfcheck.html sfcheck] - run CCP4Online sfcheck | * [http://www.ccp4.ac.uk/dist/html/sfcheck.html sfcheck] - run CCP4Online sfcheck | ||
* [http://sts.bioengr.uic.edu/castp/index.php CASTp] - webserver for identification and measurements of surface accessible pockets as well as interior | * [http://sts.bioengr.uic.edu/castp/index.php CASTp] - webserver for identification and measurements of surface accessible pockets as well as interior | ||
* [http://www.biochem.ucl.ac.uk/bsm/ligplot/manual/man8.html DIMPLOT ]- Interactions between monomers of a dimer | * [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://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.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) | ||
Latest revision as of 09:54, 27 August 2010
- 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. There is also LigPlot+ at http://www.ebi.ac.uk/thornton-srv/software/LigPlus/; the PDBsum server internally runs ligplot and returns pdf files; non-released PDB files can be handled using the "generate" option in the left panel
- 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
- SURFACE and AREAIMOL - (ccp4) -surface programs
- VOIDOO - look for interior cavities
- VADAR - (Volume, Area, Dihedral Angle Reporter)