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simomarsili
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Bayesian entropy estimation in Python - via the Nemenman-Schafee-Bialek algorithm
Incorporation of conformational space profile into molecular representation learning, and its application to drug discovery, including virtual screening, target identification, and QSAR.
Scaffold decoration and fragment linking with chemical language models and RL
Diffusion model based protein-ligand flexible docking method
Hackable and optimized Transformers building blocks, supporting a composable construction.
A single model for all your molecular design tasks
Quantum chemistry program executor and IO standardizer (QCSchema).
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
Chemoinformatics toolkit with support for inorganic molecules
The official PyTorch implementation of PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecule Generation.
(Kuhn-Munkres) numpy implementation, rectangular matrix is supported (|X| <= |Y|). 100x100000 in 0.153 s.
A python package for performing GROMACS simulation ensembles
A command line application to launch molecular dynamics simulations with OpenMM
Absolute solvation free energy calculations with OpenFF and OpenMM
Open-source tool for synthons-based library design.
some examples code of Rdkit to generate a virtual library from specified SMARTs reactions and reactants/building blocks
Python tool for generate fingerprints of a molecule
Derive ΔG for single residues from HDX-MS data
A lightweight, object-oriented finite state machine implementation in Python with many extensions
some example GROMACS .mdp files for setting up and performing moleculecular dynamics in GROMACS
Practical Python Programming (course by @dabeaz)
Code Repository for Machine Learning with PyTorch and Scikit-Learn
Explainer for black box models that predict molecule properties