HIbrahim's Projects
Dynamic pharmacophore modeling of molecular interactions
This is a simple GUI for protein simulations with Gromacs on Linux systems
Code to accompany "Practical Cheminformatics With Open Source Software"
EmDee: A Molecular Dynamics Laboratory
Python / Molecular Dynamic Simulation Analysis Scripts
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/
Gromacs performance benchmarking on different HPC platforms
Protocols for running MD simulations in Gromacs
gromacs short scripts
Trusted force field files for gromacs
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
Benchmark interpretation of QSAR models
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.
Ready-to-use tools that are always needed in the Lab
A high-throughput data extraction package for LC-MS data.
Python optimisation of atomistic ligand charges to maximize receptor binding affinity
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Python Scripts, CLI, and modules for analyzing protein-ligand trajectories
Simple Node Editor is just that. Very basic minimal code for implementing a node graph or editor using PySide2. All nodes are built from using QGraphicsItems.
Model equations to simulate monoclonal antibody production in a fed batch bioreactor
Listing of papers about machine learning for proteins.
Cloud-based molecular simulations for everyone
A hierarchical, component based molecule builder
Material related to the course in Molecular Dynamics
Command line interface for MDAnalysis
A repository for MDAnalysis talks
mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods