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.

App ID
Method name
Commercial software
Free software
1456
gnina+pharmit

https://sourceforge.net/projects/pharmit/

https://github.com/gnina/gnina

1454
RFL-Bambu

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

1451
Hit Stream
  • Molecular Operating Environment (MOE)
  • Glide (Schrödinger)
  • Q-Chem
  • Gaussian
  • AutoDock Vina
  • Protein-Ligand ANT System (PLANTS)
  • GROMACS
  • Dock 3.7 (Kuntz Group UCSF)
1450
Hybrid

In-house

GROMACS and AMBER (if required).

1448
Hybrid: High-throughput docking coupled with reevaluation of top hits & docked poses

Schrodinger's Drug Discovery Suite, BioSolvIT SeeSAR, MolSoft ICM.

None.

1447
Ultra-Large Scale Virtual Screening & Docking

Schöringer SMD Suite, GRID, Flap, BioGPS

CmDock, PyMOL, Q, R, Python, RDKit, KNIME, ProBiS

1444
One-shot Batch Bayesopt

None

Python Autodock vina pytorch, gpytorch, botorch

1443
CMOD Design

Gaussian

OpenMM, OpenForceField, Gromacs, MDAnalysis, AmberTools, Autodock Vina, Ledock, Plants, internally developed machine learning models (MILCDock)

1442
Hydration site analysis guided virtual screening campaign

Molsoft ICM-Pro

CCG MOE

AMBER

KNIME server

Python + libraries (OpenMM, RDKit, pandas, matplotlib, numpy)

PyRod

1439
Dynamic 3D Pharmacophores

InteLigand - LigandScout

CCG - MOE

Schrodinger - Desmond

CCDC - GOLD

OpenEye - Szybki

PyRod

1438
FEgrow

N/A

FEgrow: https://github.com/cole-group/FEgrow

gnina: https://github.com/gnina/gnina

DeLinker: https://github.com/oxpig/DeLinker

RDKit: https://github.com/rdkit/rdkit

SOMD: https://github.com/michellab/Sire

1434
RLMM

OpenEye

RDKit, OpenMM, AMBER20

1432
Tiered screening incorporating molecular shape, pharmacophore features, docking and clustering
  • 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
1431
Evolutionary chemical binding similarity

BIOVIA Discovery Studio Client

RDKit, AutoDock VINA, AutoDock, graphDelta, Gromacs, gmx_MMPBSA

1430
Massive Library Screening using Structurally-Augmented Drug-Target Interaction (DTI) prediction models

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.

1429
Artificial Intelligence-driven Optimization of Ligands (AIOLI)
  • Pipeline Pilot (BioVia)
  • Spark, Ignite (Cresset)
  • Glide, ABFEP (Schrodinger)
  • FlexX, Ftrees, SpaceLight (BioSolveIT)
  • Synthesia (Univ. Hamburg) -> free for academic use
  • Arthor (NextMove)
1428
Synthon-GA

Glide, SmallWorld, FTrees

Synthon-GA

1425
Frag2Hits

Glide, to additionally veryfy nominated hits

Autodock, FTMap, LigTBM, ReLeaSE

1422
Multi-scale Drug-Protein Interaction prediction (M-DPI)

Python, Torch, RDKIT, Biopython, P2Rank

1421
FRASE-bot

Schrodinger, Pipeline Pilot

RDKit, Keras/TensorFlow

1419
SCORCH screening pipeline

StarDrop

Autodock, PSOVina2, GWOVina, RF-Score-VS v2, SCORCH, Osiris DataWarrior, PDB2PQR, OpenBabel, RDKit

1418
V-SYNTHES

ICM-Pro is provided by MolSoft.

RDKit, KNIME

1414
Drugit

Foldit/Rosetta/RDKit/ZINC API/BCL/OpenBabel

1413
Function-site interaction fingerprint method

IChem (from Dr. Rognan group)

Autodock Vina (Docking)

Acemd (MD simulations)