Alexander Matthew Payne

Ph d Candidate @Tri-Institutional Phd Program In Chemical Biology Tpcb

New York, NY, US

ASAP: Open Science Drug Discovery for the Prevention of Future Pandemics”- Contributed to a Python pipeline using OpenEye to evaluate strategies for docking molecules to the Fragalysis dataset of SARS-CoV-2 Main Protease ligands (https://github.com/choderalab/asapdiscovery)- Explored methods of transferring knowledge of molecule activity to related viral targets- Collaborated with an international team“Pursuing Allosteric Activators of an Ion Channel on the Road to a Parkinson\'s Disease Therapeutic”- Built an improved protein model using ChimeraX, Coot, and Phenix, and set up simulations using CHARMM-GUI- Ran simulations of the protein using OpenMM on Folding@home (F@h) and analyzed with MDTraj- Maintained GitHub repositories of simulation setup and analysis - choderalab/tmem175-allostery-analysis-CL: local simulations and analysis in preparation for F@h - choderalab/fah-analysis-tmem175: analysis of F@h data using PyEMMA - choderalab/enhanced-sampling-tmem175: setup and analysis of some enhanced sampling simulations“Structural Analysis of a Dynamic Single-Pass Transmembrane Protein”, in collaboration with the Huang Lab at WCM- Collected CryoEM data and extensively classified using Relion and CryoSPARC, with a paper submitted“Computational Probing of Structural Determinants for Deficient Rhodopsin Dimerization in Retinitis Pigmentosa”- Analyzed Martini simulations of Rhodopsin mutants using Tcl/Tk (a scripting language) and Python and visualized the results with VMD- Determined differences in dimerization contacts between mutants, earning co-authorship in Khelashvilli 2021

The University of North Carolina at Chapel Hill

Bachelor’s Degree, Biology, Chemistry

Delaware County Christian School

High School Diploma

Tri-Institutional PhD Program in Chemical Biology (TPCB)

Doctor of Philosophy - PhD, Chemical Biology