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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.
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.
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.
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.
Quick Vina 2 is a fast and accurate molecular docking tool, attained at accurately accelerating AutoDock Vina. This fork of QVina 2 adds changes that allow it to run as part of DockingFactory.
An SGC Open Chemistry Networks Project (number 20) dedicated to finding hits vs CHIKV nsp2 helicase based on a Virtual Screen of Enamine REAL compounds.
A Bash script to submit batch jobs to ORCA, OpenBabel, MGLTools, and Autodock Vina. Automatically checks for syntax errors in ORCA input files, and can also identify ORCA runtime crashes. Organizes log files into individual directories, and creates an easy to read results summary text file. Created by Rac Mukkamala
Automated pipeline for pharmacophore based virtual screening using the interface of pharmit interactive exploration of chemical space and ADMET analysis using ADMETLAB 2.0 API