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addnewresidue.py

This code adds custom-made amino acids to the GROMACS forcefield directory.

alchemlyb

the simple alchemistry library

amberff-in-namd

ambertutorials

autoenthalpy

An automated workflow for the absolute binding enthaply calculation of host-guest systems

chimera

Scripts for UCSF Chimera and PyChimera, for data analysis and graphics generation

dynden

freeenergy_tutorial

A tutorial on free energy simulations using the GROMACS software

gromacstutorials

ipbsa

iPBSA minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods. The algorithm is based on a freely available AmberTools18 which can be easily installed via conda

meeko

Interfacing RDKit and AutoDock

moleculardockingtutorials

Molecular docking scripts for virtual screening studies

molmodsim-md-theory-lesson-novice

Some practical theoretic background needed for running MD simulations

openbpmd

qubekit

Quantum Mechanical Bespoke Force Field Derivation Toolkit

smi2sdf3d

3D diverse conformers generation using rdkit

ssbind

umbrellasampling

This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.

uni-gbsa

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.

useful_rdkit_utils

Some useful RDKit functions

vfu

Streamlined version of VirtualFlow combining both VFVS and VFLP

vfvs

VirtualFlow for Virtual Screening