My protein doesn't have complex structure . So, right now i am doing homo-logy modelling with other protein (with 74% sequence identity). Does, this methods give us the idea to know the active site cavity and calculate its volume.
Hi you can use sitemap (schrodinger), a pymol plugin called PocketPicker: http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/index.htm, CASTp http://sts.bioengr.uic.edu/castp/, LigASite: http://www.bigre.ulb.ac.be/Users/benoit/LigASite/index.php?home, PDBeMotif: http://www.ebi.ac.uk/pdbe-site/pdbemotif/ , metaPocket: http://metapocket.eml.org/, 3DLigandStie: http://www.sbg.bio.ic.ac.uk/~3dligandsite/ , FINDSITE: http://cssb.biology.gatech.edu/findsite, Pocket-Finder: http://www.modelling.leeds.ac.uk/pocketfinder/, CAVER: http://www.caver.cz/....