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

1212

Frag2Hits

Glide by Schrödinger

FTMap server (https://ftmap.bu.edu/), RDKit

1210

CReM

FTrees

CReM, Autodock Vina, Smina, gnina, DeepDock

1209

DeepDocking, neural network atomistic force fields, molecular dynamics, thermodynamic integration, free energy methods, de novo generative models

Glide, ICM, OpenEye toolkit, AMBER

OpenChem, torchani, pytorch, Autodock-GPU

1208

Sequential fragment-based/HTS docking hit identification

none

GROMACS, gnina, vina, qvina-w, VMD, Pymol, python

1207

Dynamic 3D Pharmacophores

LigandScout (Inte:Ligand, Austria) GOLD - (The Cambridge Crystallographic Data Centre, UK) Szybki (OpenEye, NM, USA)

Desmond (deshaw research, NY, USA) OpenMM (https://openmm.org/)

1206

Deep integration of physics and machine learning based methods for accurate molecule ranking

Autodock Vina, Autodock4, Ledock, rDock, PLANTS, OpenMM, internally developed machine learning models (omission of name for blind review)

1205

High-throughput docking, with rescoring using structural waters and ligand conformational strain

Glide/Maestro/Drug Discovery suite (Schrödinger, Inc), SeeSAR (BioSolveIT), BIOVIA Pipeline Pilot.

N/A

1204

Ligand Design - Massive Library Screening

MatchMaker

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.

1203

MIF-based Virtual Screening

GRID, FLAP, BioGPS, VolSurf+

1202

ProCare

OpenEye Scientific Software (Santa Fe, NM 87508, U.S.A. https://www.eyesopen.com), Corina (Molecular Networks GmbH, 90411 Nürnberg, Germany. https://mn-am.com), HYDE (BioSolveIT GmbH, 53757 Sankt Augustin, Germany. https://www.biosolveit.de)

IChem (free academic license), ProCare, DeLinker, Protoss (free academic license), PLANTS (free academic license), RDKit

1201

RosettaLigand, RosettaLigandEvolution, BCL

Rosetta Suite, Biology and Chemistry Library (BCL), PyMOL, Python– RDKit and other free libraries

1200

MM docking, MD, de novo design, fingerprint searching will be used

MOE

1198

DeepAffinity

https://github.com/Shen-Lab/DeepAffinity (GPL-3.0), https://github.com/Shen-Lab/CPAC (GPL-3.0), https://github.com/Shen-Lab/Drug-Combo-Generator (Apache-2.0), https://github.com/ccsb-scripps/AutoDock-Vina (Apache-2.0), https://www.ks.uiuc.edu/Research/namd/license.html (Non-Exclusive, Non-Commercial Use License)

1195

VirtualFlow

Maestro (protein preparation)

VirtualFlow, AutoDock Vina, QuickVina, Smina, Plants, GWOVina

1193

Schrödinger suite

REINVENT, scikit-learn

1191

Hybrid

in-house

Gromacs if MD is needed

1188