suleymanselim
I am a PhD student at the Department of Biochemistry at the University of Oxford. My interests broadly focuses on protein dynamics and drug design.
Oxford
Pinned Repositories
addNewResidue.py
This code adds custom-made amino acids to the GROMACS forcefield directory.
alchemlyb
the simple alchemistry library
AMBERff-in-NAMD
AmberTutorials
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.
suleymanselim's Repositories
suleymanselim/MolecularDockingTutorials
Molecular docking scripts for virtual screening studies
suleymanselim/UmbrellaSampling
This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.
suleymanselim/AmberTutorials
suleymanselim/addNewResidue.py
This code adds custom-made amino acids to the GROMACS forcefield directory.
suleymanselim/alchemlyb
the simple alchemistry library
suleymanselim/AMBERff-in-NAMD
suleymanselim/AutoEnthalpy
An automated workflow for the absolute binding enthaply calculation of host-guest systems
suleymanselim/chimera
Scripts for UCSF Chimera and PyChimera, for data analysis and graphics generation
suleymanselim/DynDen
suleymanselim/freeenergy_tutorial
A tutorial on free energy simulations using the GROMACS software
suleymanselim/GromacsTutorials
suleymanselim/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
suleymanselim/Meeko
Interfacing RDKit and AutoDock
suleymanselim/molmodsim-md-theory-lesson-novice
Some practical theoretic background needed for running MD simulations
suleymanselim/OpenBPMD
suleymanselim/QUBEKit
Quantum Mechanical Bespoke Force Field Derivation Toolkit
suleymanselim/smi2sdf3d
3D diverse conformers generation using rdkit
suleymanselim/ssBind
suleymanselim/Uni-GBSA
An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
suleymanselim/useful_rdkit_utils
Some useful RDKit functions
suleymanselim/VFU
Streamlined version of VirtualFlow combining both VFVS and VFLP
suleymanselim/VFVS
VirtualFlow for Virtual Screening