Emmett M. Leddin

PhD | Computational Biochemistry

Publications • Education • GitHub Projects • Tutorials • Website Maintained • Hackathons • CV • External Profiles

Publications

Human polymerase kappa, with zoom of active site and values for WT and Y432S mutant

February 2024 (preprint)

Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ

ChemRxiv

left: catalytic and allosteric binding sites, right: secondary structure of APOBEC3B

December 2023

Computational drug discovery of an inhibitor of APOBEC3B as a treatment for epithelial cancers

J. Biomol. Struct. Dyn.

schematic diagram of Group 1 POT1 variants

December 2022

Population-based analysis of POT1 variants in a cutaneous melanoma case–control cohort

J. Med. Genet. MedRxiv

residues with large energy changes in TET2

August 2022

The impact of inflammation-induced tumor plasticity during myeloid transformation

Cancer Discovery PubMed Central

workflow starting with HyDn-SNP-S going to both MD and the PFAM database, looking for compensatory mutation, and returning to MD

May 2022

Computational Compensatory Mutation Discovery Approach: Predicting a PARP1 Variant Rescue Mutation

Biophys. J. BioRxiv

network analysis communications between the RdRp regions of RNA, NSP8-a, NSP8-b, NSP7, Polymerase, NiRAN, and Interface

April 2022

Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase

J. Chem. Inf. Model. ChemRxiv

a 3-part image with text sequence/structure alignment, QM/MM, and electron localization function with a sequence, 3 PDB structures, and an active site

June 2021

Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations

J. Chem. Theory Comput. ChemRxiv

stepwise oxidation of 5mC to 5hmC to 5fC to 5caC

October 2019

Comparison of DNA and RNA Substrate Effects on TET2 Structure

APCSB PubMed Central

a nucleic acid backbone with 5mC the middle where coloration is based on RNA disfavored and DNA preferred as red to both tolerated as purple and RNA preferred and DNA disfavored as orange

November 2018

Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA

Biochemistry PubMed Central

two-part image with a PDB structure to the left and the extension activity to the right

July 2018

Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase kappa

Chem. Res. Tox. PubMed Central

Education

Medical

Anticipated May 2026

Current MS2

Doctoral

May 2022

Doctor of Philosophy in Chemistry
Concentration in Physical Chemistry
Dissertation: Computational Modeling of Cancer-Related Mutations in DNA Repair Enzymes Using Molecular Dynamics and Quantum Mechanics/Molecular Mechanics

Dissertation

Baccalaureate

May 2017

Bachelor of Science in Chemistry (ACS Certified)
Bachelor of Arts in Psychology

GitHub Projects

Computational Chemistry Website

atoms showing vacuum, implicit, and explicit solvation

My website with guides for getting started with UNIX, AMBER, simulation analysis, and R.

GitHub

Research Scripts

scatterplot

Different run and analysis scripts as described on the Computational Chemistry Website.

GitHub

PDBXYZ and XYZPDB

protein structure

Scripts to convert between PDB to XYZ files, without using the existing TINKER programs for conversion.

GitHub

Vim Cpptraj

vim screenshot

Syntax highlighting for cpptraj in vim.

GitHub

VSCode Cpptraj

VS Code screenshot

Syntax highlighting for cpptraj in Visual Studio Code.

GitHub

Atom Cpptraj

Atom screenshot

Syntax highlighting for cpptraj in the Atom text editor.

GitHub

THRIVE Lifeline Resource Table

table screenshot

A table rendered using the DT package for RMarkdown.

GitHub

THRIVE Lifeline Resource App

shiny table screenshot

An R Shiny app to render a CSV.

GitHub

Tutorials

LICHEM Tutorial

A tutorial for performing quantum mechanics/molecular mechanics (QM/MM) simulations with LICHEM.

GitHub

OpenMM and MDAnalysis Tutorial

A tutorial for setting up and analyzing molecular dynamics simulations with Python.

GitHub

Website Maintained

THRIVE Lifeline

screenshot of THRIVE Lifeline site index

An RMarkdown-based site for THRIVE Lifeline, a text-based crisis hotline staffed by people in STEMM with marginalized identities.

Website

Hackathons

Real-World Issue Challenge

AccessMap homepage which shows a map with pins

First place
2021 oSTEM Hackathon Project with the Spoopy team to address the issue of college campus inaccessibility.

GitHub

Crisis Resources Challenge

presentation slide for Queers in Crisis

Third place
2020 oSTEM Hackathon Project with the Queers in Crisis team to modify the presentation of the oSTEM website's crisis resources.

GitHub

Voter Literacy App Challenge

app tile layout

First place
2019 oSTEM Hackathon Project with the Non-Conformist Narwhal team to create a phone app of voter resources for LGBT Detroit.

GitHub

CV

If the PDF doesn't load, you can access it through my CV GitHub repository.