Jeff Warrington's repositories
REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
chemprop
Message Passing Neural Networks for Molecule Property Prediction
CarsiDock
Official repo of CarsiDock proposed by CarbonSilicon AI.
ray
Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a set of AI Libraries for accelerating ML workloads.
ExampleNotebooks
Notebooks demonstrating how to do simple tasks related to free energy calculations.
Lomap
Alchemical mutation scoring map
plumed2
Development version of plumed 2
AutoDock-Vina
AutoDock Vina
DynamicBind
repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
pmx
Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
SAFEP_tutorial
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
FrameDiPT
FrameDiPT: an SE(3) diffusion model for protein structure inpainting
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
skills-introduction-to-github
My clone repository
Dock-MD-FEP
Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.
perses
Experiments with expanded ensembles to explore chemical space
making-it-rain
Cloud-based molecular simulations for everyone
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
gnina
A deep learning framework for molecular docking
molpal
active learning for accelerated high-throughput virtual screening
wedap
Weighted Ensemble Data Analysis and Plotting
pdb2pqr
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
espsim
Scoring of shape and ESP similarity with RDKit
caviar
// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition
pdbfixer
PDBFixer fixes problems in PDB files
Blackgrass-Genome-Project
Genome sequencing of blackgrass and Non-target site herbicide resistance