HIbrahim's repositories
MDPerTool_GUI
Perturbation based Allosteric Pathway Finder
af2_conformations
A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2
awesome-python-chemistry
A curated list of Python packages related to chemistry
Cheminformatics-Teaching-Material
Resources, Code, and Other things I use to teach Cheminformatics.
Cheminformatics-Tutorials
Practical Cheminformatics Tutorials
DeepSCM
A convolutional neural network model to predict spatial charge map (SCM) score, a molecular dynamics simulation-based model to predict antibody viscosity.
docking_automation
Docking_Automation
dynophores
Dynamic pharmacophore modeling of molecular interactions
EFMC
Code to accompany "Practical Cheminformatics With Open Source Software"
Gromacs-Utilities
gromacs short scripts
ibenchmark
Benchmark interpretation of QSAR models
Lab-Releated-Stuffs
Ready-to-use tools that are always needed in the Lab
LaCyTools
A high-throughput data extraction package for LC-MS data.
mdciao
mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
pharmd
MD pharmacophores and virtual screening
poster-presentations
Storing soft copies of poster presentations along with QR code links for easy access
pymol-color-alphafold
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
python-fire
Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.
qMSM_tutorial
A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
Reactor-data-parsing-and-analysis
Parsing and data analysis with BioLector microbioreactor data.
tobit_analysis
Simple Tobit regression in python
tobit_pytorch
Low API tensorflow implementation of censored regression Tobit model.
toxsmi
Toxicity prediction models
Troubleshooting_on_lab
The most common problems and their solutions on UBUNTU
useful_rdkit_utils
Some useful RDKit functions