Python notebooks for basics of ML in Digital Chemistry to building advanced MLIPs and physics-based descriptors for DFT predictions.

CosolvKit is a versatile tool for cosolvent MD preparation and analysis

This repository contains all the input files used for the L-ABF-OPES paper: "L-ABF-OPES: Absolute Binding Free Energy Calculations Using Local Adaptively Biased Force and On-the-Fly Probability Enh…

A Markov State Model of Solvent FeaturesReveals Water Dynamics in Protein-ProteinBinding

Utility for converting XTC trajectory step numbers to frame numbers.

For using the pyemma package released by Frank Noe efficiently for my projects

tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors

resources for faculty

Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.

Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.

Computing Diffusion Coefficients in Macromolecular Simulations: The Diffusion Coefficient Tool for VMD

AI for Science

Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

C-library for calculating Solvent Accessible Surface Areas

A Python/Fortran order parameter analysis library

::A Python script to calculate and visualize the F4 order parameter from GROMACS trajectory::

A Python script to calculate F3 order parameter from GROMACS trajectory

A fast, OpenMP parallelised C++ package that calculates the radial distribution of various local order parameters for water droplets from MD trajectories.

🚰 A tool to characterize the local structure of liquid water by geometric order parameters.

A tool to analyse the distribution of water molecules in the first solvation shell of certain molecules.

Data and analysis scripts used in Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

a library for massive analyses of internal voids in biomolecules and ligand transport through them

Scripts to prepare and analyze molecular dynamics simulations

Python module for identification of conserved water molecules from molecular dynamics trajectories.

Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis

PyRod - Tracing water molecules in molecular dynamics simulations