HIbrahim's repositories
mbuild
A hierarchical, component based molecule builder
Ligand-Optimiser
Python optimisation of atomistic ligand charges to maximize receptor binding affinity
conveyorlc
A pipeline to do virtual screening
nanopore-electrowetting-scripts
:microscope: Scripts for analyzing molecular dynamics trajectories of nanopores under the influence of an external electric field
MDtools
Tools and scripts developed for MD research
openmm-plumed-tests
Alanine dipeptide OpenMM-Plumed test
openmm-scripts-amoeba
:microscope: OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field
gmx_protocols
Protocols for running MD simulations in Gromacs
Model-generation
Python scripts to generate an MD-ready model from smiles strings
Notebooks
Assorted IPython Notebooks
parallel_gold
Run GOLD in parallel
Chem324
Introduction to Quantum Mechanics Lecture Notes (Chem324, Fall 2019)
DashMD
Real time monitoring and visualization of Amber MD simulations
AMIDD
Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)
pdbe-api-training
Interactive Python notebooks for PDBe API training
tutorials
Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.
md-course
Material related to the course in Molecular Dynamics
autodock-vina_scripts
Autodock vina command line scripts
Hbind
Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka et al. (2018) J. Computer-Aided Molec. Design
pyside2-threading
Basic example of using PySide2 and putting a worker object in a different thread to not block the GUI on the main thread.
RNA_in_water
RNA Molecular Dynamics Simulation in water and how changes on temperature and ions affect structure
plants-scripts
scripts to work with PLANTS docking software and its output
allopred
Predict allosteric pockets on proteins
structurework
programs and scripts for molecular structure analysis
easyGromacs
This is a simple GUI for protein simulations with Gromacs on Linux systems
openmm-journal-club
:notebook: Overview the OpenMM Molecular Dynamics Engine
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
The-Databases-for-Drug-Discovery
The Databases for Drug Discovery (DDD)
tcr-pmhc-model
Scripts for modelling TCR:pMHC structures