CHALLENGE #2 – COMPUTATIONAL METHODS
Here is a list of all computational methods used for hit identification in CACHE challenge #2. Click on the application ID for more details.
AutoDock Vina 1.1.2, AutoDock Tools, Primordia, RDKit, BINANA, PaDEL Descriptors, ZINC Database, PDB Database, Alphafold EBI Database, Gromacs, Pymol, VMD, Python and Biopython
- Molecular Operating Environment (MOE)
- Glide (Schrödinger)
- Q-Chem
- Gaussian
- AutoDock Vina
- Protein-Ligand ANT System (PLANTS)
- GROMACS
- Dock 3.7 (Kuntz Group UCSF)
Schrodinger's Drug Discovery Suite, BioSolvIT SeeSAR, MolSoft ICM.
None.
Schöringer SMD Suite, GRID, Flap, BioGPS
CmDock, PyMOL, Q, R, Python, RDKit, KNIME, ProBiS
Gaussian
OpenMM, OpenForceField, Gromacs, MDAnalysis, AmberTools, Autodock Vina, Ledock, Plants, internally developed machine learning models (MILCDock)
Molsoft ICM-Pro
CCG MOE
AMBER
KNIME server
Python + libraries (OpenMM, RDKit, pandas, matplotlib, numpy)
PyRod
InteLigand - LigandScout
CCG - MOE
Schrodinger - Desmond
CCDC - GOLD
OpenEye - Szybki
PyRod
N/A
FEgrow: https://github.com/cole-group/FEgrow
gnina: https://github.com/gnina/gnina
DeLinker: https://github.com/oxpig/DeLinker
- Molecular Operating Environment (MOE) by the Chemical Computing Group
- OpenEye- fastROCS (hit identification using shape information), OMEGA (generating conformations), MakeReceptor (preparing binding pocket for docking) and FRED (docking)
- Pipeline Pilot (Biovia)
- Kalign
- In-house MoPBS pharmacophore generation software
- In-house VS streamlining software DataPype
BIOVIA Discovery Studio Client
RDKit, AutoDock VINA, AutoDock, graphDelta, Gromacs, gmx_MMPBSA
MatchMaker (Cyclica Inc.)
Python-based ML stack (PyTorch, scikit-learn)
BioPython computational biology toolkit
RD-Kit computational chemistry toolkit
Various structural biology tools for structural analysis and visualization, including P2Rank, NGL viewer, Autodock Vina.
- Pipeline Pilot (BioVia)
- Spark, Ignite (Cresset)
- Glide, ABFEP (Schrodinger)
- FlexX, Ftrees, SpaceLight (BioSolveIT)
- Synthesia (Univ. Hamburg) -> free for academic use
- Arthor (NextMove)
Python, Torch, RDKIT, Biopython, P2Rank
StarDrop
Autodock, PSOVina2, GWOVina, RF-Score-VS v2, SCORCH, Osiris DataWarrior, PDB2PQR, OpenBabel, RDKit
IChem (from Dr. Rognan group)
Autodock Vina (Docking)
Acemd (MD simulations)