Dr. Alexander Bayden

Current Research

I am involved in both molecular modeling and code development. These activities are hard to separate, because most of the code I develop is used to automate the modeling work.

Developing Radiation Sensitizers for the Treatment of Glioma Tumors

Recent experiments have shown that the attachment of SHP2 to EGFR can help in radiation treatment of glioma tumors. We are developing an activator of SHP2.

Prediction of Which Tyrosines Get Nitrated By Ionizing Radiation

Antibiotics Discovery

O- acetylserine sulfhydrylase-A (OASS-A) catalyzes the last reaction in the biosynthesis of cysteine in bacteria and plants. It is inhibited by another protein, serine acetyltransferase (SAT). We are trying to discover novel antimicrobial agents by searching 3D databases for small molecule analogs of SAT that can reversibly inhibit OASS-A.

Discovery of Antiviral Agents

We are searching 3D databases for the inhibitors of parainfluenza fusion protein.

Writing a GUI Interface for the HINT Program

The hint!® program translates a large set of experimentally obtained partition coefficients into a free energy interaction model for biomolecules. Unfortunately it is non-trivial to use hint!® from the command line. That is why we are developing a GUI for hint!® using wxPython.

Building a Computational Titration Web Application

We a re building a hint!®-based web application for analysis of protonation states in protein-ligand complexes.

You can try Computational Titration at the web-server http://hinttools.isbdd.vcu.edu/CT

Visualization of MD Trajectories

We are experimenting with a novel way to visualize molecular dynamics trajectories, that goes beyond traditional 2D RMSD plots.

Automating the Work of Other Group Members

I am helping to speed up the work of other group members by writing various scripts and programs to automate calculations. This can make a difference between analyzing tens of compounds and thousands of compounds.