FrAG-PELE. Fragment-based Automatic Growing.¶
FrAG a new tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand conformational space.
The general workflow starts with the system preparation, where core and fragment are put together, followed by several growing stages, where various parallel Monte Carlo simulations are performed while increasing linearly the fragment characteristics. In each stage a clustering and spawning is done to trigger the next growing stage. Finally, a simulation analysis package scores best poses and retrieved its PDBs.
FrAG is build on top of Protein Energy Landscape Exploration (PELE) Software.
Requirements (you can use other versions of all modules, but they have not been tested with the newest version):
- Python >= 3.5.6
- AdaptivePELE >= 1.6.1
- Schrödinger’s Python = 2.7.13
- Schrödinger Preparation Wizard
- Biopython = 1.70
- Prody >= 1.10.10
- Pandas >= 1.0.1
- rdkit = 2019.09.3
Installation¶
- Installation
- Getting Started
- How to do it?
- Previous Requisites
- Growing of a fragment to a core
- Growing of two fragment to the same core
- Growing of a fragment to a previously grown fragment
- All together
- Launch simple FrAG-PELE simulation
- Growing a fragment specifying direction
- Growing through BOND-LIKE selection
- Growing by double or triple bonding
- How to do it?