Pinned Repositories
AbAgInterface
shrec22_proteinLigandBenchmark
Dataset and evalutaion tools of the Shrec 2022 contest on protein-ligand binding site recognition
SiteFerret
Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest
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.
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 .
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.
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)
lucagl's Repositories
lucagl/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 .
lucagl/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)
lucagl/codes_thesis
Raw fortran codes used to produce most of the results of my PhD thesis
lucagl/KMC_pattern
Kinetic MC code describing the evolution of a two phases system: a solid cluster and a cloud of mobile units.
lucagl/mpdb2xyzr
Converts mpdb files to a set of frames in xyzr format given a reference PQR file
lucagl/NS_pocket
Python interface for the pocket detection method of the NanoShaper software with volume ranking
lucagl/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.