Name: HIbrahim
Type: User
Company: Marmara University/ Computational Biology and Bioinformatics Lab
Bio: focuses on applying atomistic molecular simulation methods to complex problems in biology and human health
Location: Göztepe/Kadıköy/İstanbul
Blog: https://www.linkedin.com/in/halil-ibrahim-%C3%B6zdemir-951197b9/?locale=en_US
HIbrahim's Projects
Run GOLD in parallel
download and prepare a pdb file for docking wth Vina-flavoured algorithms
Interactive Python notebooks for PDBe API training
a collection of scripts and files to help in PDB retrieval for various projects
analyse PDB files, run molecular-dynamics & analyse trajectories
A simple Python library to generate model peptides
MD pharmacophores and virtual screening
scripts to work with PLANTS docking software and its output
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315
Storing soft copies of poster presentations along with QR code links for easy access
Custom Pressure Reporter for OpenMM
A collection of useful tutorials for Protein Science
Personal library for analyzing protein structures and trajectories produced from MD or MC simulations.
Examples and data for performing path similarity analysis (PSA).
python opengl protein viewer
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
Some notes (cookbook) for pyMol. Protein Crystallography course.
Pymol ScrIpt COllection (PSICO)
Collected scripts for Pymol
A Python API for the RCSB Protein Data Bank (PDB)
Automatically exported from code.google.com/p/pyplif
Python implementation of the fast rmsd and optimal rotation matrix method by Douglas Theobald and Pu Liu
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
Basic example of using PySide2 and putting a worker object in a different thread to not block the GUI on the main thread.
Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.
A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
Quantum Mechanical Bespoke Force Field Derivation Toolkit
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