Automatic identification of important interactions and interaction-frequency-based scoring in protein-ligand complexes
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Updated
Oct 25, 2021 - Jupyter Notebook
Automatic identification of important interactions and interaction-frequency-based scoring in protein-ligand complexes
The aim of this project was to create a computational pipeline for the identification of drug candidates for JAK-family kinases, which are a group of proteins involved in inflamatory diseases such as rheumatoid arthritis or psoriasis.
A Framework for Virtual Screnning
A quick and dirty virtual screening task for potential ligands of Flavobacterium johnsoniae Tyrosine Ammonia Lyase (FjTAL)
DockingInterface is a Python wrapper for open-source molecular docking programs: Autodock Vina, Smina, QVina2, and rDock.
AutoDock Vina is one of the fastest and most widely used open-source docking engines. It is based on a simple scoring function and rapid gradient-optimization conformational search. It was originally designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab. This fork of Vina adds changes that allow it to be a part of DockingFactory.
Python program to run several PELE simulations in a very authomaticall way
Prediction model used in the paper: Accelerated Design of Near-Infrared-II Molecular Fluorophores via First-Principle Understanding and Machine Learning.
VSpipe - A pipeline to carry out virtual screenings
Maximal Unbiased Benchmarking Datasets for Histone Deacetylases and Sirtuin Family
Smina is fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. This fork of Smina adds changes that allow it to run as a part of DockingFactory.
Interactive web app developed using dash and python. Deployed on Heroku.
Principal Component Analysis with Python
Docking Factory is a tool to automate molecular docking runs on an HPC cluster using the Dask framework. DockingFactory provides unified way of running molecular docking with different software backends: AutoDock Vina, Smina, Qvina2, and rDock.
Course schedule from experience as a selected Undergraduate Teaching Assistant at the University of Pittsburgh course, BIOSC 1540 - Computational Structural Biology, taught by Dr. Jacob Durrant.
MIPT 2019 Bachelor's project "Pipeline for search of off-target ligand connections"
Reaction-informed Fusion of Fragments (RiFF
Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
Software for performing Automatic Ligand-guided Backbone Ensemble Receptor Optimization with ICM
Prediction of Potency between Molecules and Targets by Sequence-Based Neural Network with Application in Virtual Screening
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