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Ensemble Optimizer (EnOpt) is a fast, accessible tool that streamlines ensemble-docking and consensus-score analysis.

This is a GitHub Repository containing the data and code used for a thorough comparison of 11 ligand binding site prediction tools

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.

overview of datasets for ML in chemistry

Automated Adaptive Absolute alchemical Free Energy calculator

A unified framework for machine learning collective variables for enhanced sampling simulations

A Machine Learned Molecular Mechanics Force Field with integration into GROMACS and OpenMM

A minimal PyTorch implementation of probabilistic diffusion models for 2D datasets.

Interface for AutoDock, molecule parameterization

CosolvKit is a versatile tool for cosolvent MD preparation and analysis

We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU approach (http://pomalab.ippt.pan.pl/GoContactMap/).

Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.

Python package for graph neural networks in chemistry and biology

RDKit related blog posts, notebooks, and data.

Reproducing results from "A Deep Learning Approach to Antibiotic Discovery"

The code of a graph neural network (GNN) for molecules, which is based on learning representations of r-radius subgraphs (i.e., fingerprints) in molecules.

100 Days of ML Coding

Calculate the modelability index (MODI) of a chemical dataset

Awesome De novo drugs design papers

Visual Interactive Analysis of Molecular Dynamics

Papers about Structure-based Drug Design (SBDD)

Collected scripts for Pymol

The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent func…

Some practical theoretic background needed for running MD simulations

Python package built on OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.

This repository contains everything you need to become proficient in ML/AI Research and Research Papers

binding free energy estimator 2