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