Data for benchmarking protein-ligand binding free energy calculations.
The data is organized as followed:
plb_data
├── targets.yml # list of all targets and their directories
├── <date>_<target_name_1> # directory for target 1
│ ├── 00_data # metadata for target 1
│ │ ├── edges.yml # edges/perturbations
│ │ ├── ligands.yml # ligands and activities
│ │ └── target.yml # target
│ ├── 01_protein # protein data
│ │ ├── crd # coordinates
│ │ │ ├── protein.pdb # aminoacid residues
│ │ │ └── cofactors_crystalwater.pdb # cofactors and cyrstal waters
│ │ └── top # topology(s)
│ │ │ └── amber99sb-star-ildn-mut.ff # force field spec.
│ │ │ ├── topol.itp # Gromacs ITP file
│ │ │ └── topol.top # Gromacs TOP file
│ └── 02_ligands # ligands
│ ├── lig_<name_1> # ligand 1
│ │ ├── crd # coordinates
│ │ │ └── lig_<name_1>.sdf # SDF file
│ │ └── top # topology(s)
│ │ └── openff-1.0.0.offxml # force field spec.
│ │ ├── fflig_<name_1>.itp # Gromacs ITP file : atom types
│ │ ├── lig_<name_1>.itp # Gromacs ITP file
│ │ ├── lig_<name_1>.top # Gromacs TOP file
│ │ └── posre_lig_<name_1>.itp # Gromacs ITP file : position restraint file
│ ├── lig_<name_2> # ligand 2
│ …
│ └── 03_hybrid # edges (perturbations)
│ ├── edge_<name_1>_<name_2> # edge between ligand 1 and ligand 2
│ │ └── water # edge in water
│ │ ├── crd # coordinates
│ │ │ ├── mergedA.pdb # merged conf based on coords of ligand 1
│ │ │ ├── mergedB.pdb # merged conf based on coords of ligand 2
│ │ │ ├── pairs.dat # atom mapping
│ │ │ └── score.dat # similarity score
│ │ └── top # topology(s)
│ │ └── openff-1.0.0.offxml # force field spec.
│ │ ├── ffmerged.itp # Gromacs ITP file
│ │ ├── ffMOL.itp # Gromacs ITP file
│ │ └── merged.itp # Gromacs ITP file
│ …
├── <date>_<target_name_2> # directory for target 2
…
Copyright (c) 2020, Open Force Field, David Hahn
Project based on the Computational Molecular Science Python Cookiecutter version 1.4.