HIbrahim's repositories
Example_MD_Scripts
Python / Molecular Dynamic Simulation Analysis Scripts
molecule-slide-generator
Generate images of molecules and their properties for use in presentations and reports
Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
awesome-cheminformatics
A curated list of Cheminformatics libraries and software.
cdnjs
🤖 CDN assets - The #1 free and open source CDN built to make life easier for developers.
dockop
faster docking
GaMD-OpenMM
Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/
gmx_performance_on_HPC
Gromacs performance benchmarking on different HPC platforms
gromacs_ff
Trusted force field files for gromacs
Making-it-rain
Cloud-based molecular simulations for everyone
mdacli
Command line interface for MDAnalysis
mols2grid
Chemical viewer for 2D structures of small molecules
mpl_chord_diagram
Plot chord diagrams with matplotlib
NodeGraphQt
Node graph framework that can be re-implemented into applications that supports PySide2 or PyQt5
omm_remake_forces
remaking OpenMM forces with Custom*Forces
openmm-setup
An application for configuring and running simulations with OpenMM
OpenSourceMolecularModeling.github.io
Catalog of Open Source Molecular Modeling Projects
pdb_to_pdbqt
download and prepare a pdb file for docking wth Vina-flavoured algorithms
pdbremix
analyse PDB files, run molecular-dynamics & analyse trajectories
pyball
python opengl protein viewer
pyMol-cookbook
Some notes (cookbook) for pyMol. Protein Crystallography course.
rdeditor
Simple RDKit molecule editor GUI using PySide
rdkit-scripts
rdkit scripts making life easier