Suleyman Selim's repositories
MolecularDockingTutorials
Molecular docking scripts for virtual screening studies
UmbrellaSampling
This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.
addNewResidue.py
This code adds custom-made amino acids to the GROMACS forcefield directory.
alchemlyb
the simple alchemistry library
AutoEnthalpy
An automated workflow for the absolute binding enthaply calculation of host-guest systems
freeenergy_tutorial
A tutorial on free energy simulations using the GROMACS software
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
molmodsim-md-theory-lesson-novice
Some practical theoretic background needed for running MD simulations
QUBEKit
Quantum Mechanical Bespoke Force Field Derivation Toolkit
smi2sdf3d
3D diverse conformers generation using rdkit
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