Luca's repositories
MOAD_ligandFinder
A script able to extract ligands from pdb structure(s) and remove them from the original structure. The ligands are identified according to the *valid* ligands found in the binding MOAD database. The ligand can be extracted as a pdb or as a xyz (coordinate) file. Other options such as converting the queried pdb to pqr are available .
solventExposed
A script based on NanoShaper protein surface software returning the list of atoms and residues solvent exposed (or according to a user defined probe radius)
codes_thesis
Raw fortran codes used to produce most of the results of my PhD thesis
KMC_pattern
Kinetic MC code describing the evolution of a two phases system: a solid cluster and a cloud of mobile units.
mpdb2xyzr
Converts mpdb files to a set of frames in xyzr format given a reference PQR file
NS_pocket
Python interface for the pocket detection method of the NanoShaper software with volume ranking
pickPocket
An ad-hoc hierarchical clustering algorithm able to extract and rank pockets. Extraction is based on geometrical primitives generated by the NanoShaper molecular surface software. The ranking is based on Isolation Forest anomaly detector.