Mateusz Bieniek (bieniekmateusz)

bieniekmateusz

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Location:UK

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MDAnalysis

Mateusz Bieniek's repositories

pymol-mdanalysis

Exploratory PyMOL-MDAnalysis molecular visualization system.

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absolv_test

Trying out absolv

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autodock_vina

A fork of AutoDock Vina (http://vina.scripps.edu). Updated to boost 1.70. Simplified the build process.

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fe_input_tests

SOMD and OMMT starting files

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fegrow-case-sarscov2-3toR

RBFE input files for the reproduction of the study case sarscov2-3toR in rgroup package.

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fegrow-feedstock

A conda-smithy repository for fegrow.

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fesetup

A tool for setting up free energy simulations.

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forcebalance

Systematic force field optimization.

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freesasa-python

FreeSASA Python Module

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gal

Google active learning

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mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

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openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

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openmm-ml

High level API for using machine learning models in OpenMM simulations

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protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations

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Protein-ligand-openmm-workflow

Workflow for an MD simulation of a protein-ligand complex in water with openmm

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pyDockingOrg

Rewritten version of Matteo Ferla's unofficial python API to SmallWorld

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Python_SmallWorld_API

An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)

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QUBEKit

Quantum Mechanical Bespoke Force Field Derivation Toolkit

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radical.saga

A Light-Weight Access Layer for Distributed Computing Infrastructure and Reference Implementation of the SAGA Python Language Bindings.

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Sire

Sire Molecular Simulations Framework

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somd-rbfe-protocol

Up to date protocol for preparing and running RBFE simulations (Cole's group)

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somd_example

Testing virtual sites

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staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

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ties20-feedstock

A conda-smithy repository for ties20.

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TIES_MD

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

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ties_md-feedstock

A conda-smithy repository for ties_md.

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