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

Ligand-based virtual screening with bacterial targets

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

Data set (DUDE+ Diverse) and scripts from the article: On the relevance of query definition in the performance of 3D ligand-based virtual screening

Interactive web app developed using dash and python. Deployed on Heroku.

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.

MIPT 2019 Bachelor's project "Pipeline for search of off-target ligand connections"

Taller de docking molecular y dinámica molecular

Prediction of Potency between Molecules and Targets by Sequence-Based Neural Network with Application in Virtual Screening

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.

HIV Antiviral Screening dataset

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

Analysis of COVID19 Candidates using molecular descriptors from mol2 files

PDB-CAT is a Jupyter Notebook that aims to automatically categorize the PDB structures based on the type of interaction between atoms in the protein and the ligand, and checking for any mutations in the sequence.