David Ryan Koes, PhD

Removing barriers to computational drug discovery one bit at a time

About

I have a PhD in Computer Science from Carnegie Mellon and am an Assistant Professor in the Department of Computational and Systems Biology at the University of Pittsburgh. My research is to develop novel computational algorithms and build full-scale systems to support rapid and inexpensive drug discovery while simultaneously applying these methods to develop novel therapeutics.
I use a light-themed IDE.

Contact

Suite 3064, Biomedical Science Tower 3 (BST3)
Department of Computational & Systems Biology
School of Medicine, University of Pittsburgh
3501 Fifth Avenue
Pittsburgh, PA 15260

(412) 383-5745


Publications

People

Graduate Students

Jocelyn Sunseri, Jonathan King, Paul Francoeur

Research Fellows

Matthew Ragoza

Undergraduate Students

Ajay Subramanian, Alex Visbisky, Amrita Nallathambi, Dale Erikson, Faiha Khan, Hanna Sommers, Lily Turner, Alex Ludwig (TECBio), Aaron Zheng, Sharanya Bandla, Christopher Dunstan (TECBio), Pulkit Mittal, Sara Amato, Roosha Mandal, Elisa Idrobo (TECBio), Karla Robles (TECBio), Josh Hochuli, Haiyang Huang, Noah Bastola, Anthony Tummillo, Jesus Bracho, Ethan Hain (TECBio), Jasmine Collins, Christine Grassi (TECBio), James Castiglione, Nick Rego, Jacob Riddle

Former

Teaching

MSCBIO2025: Introduction to Bioinformatics Programming in Python

An graduate-level introductory programming course with a focus on analyzing biological data.
Fall Semester

MSCBIO2065: Scalable Machine Learning for Big Data Biology

Distributed and cloud computing meets machine learning meets computational biology.
The focus is on applications rather than theory. Co-taught with Chakra Chennubhotla
Fall Semester

DiscoBio

The Drug Discovery, Systems and Computational Biology Summer Academy
An experiential summer academy for rising high school juniors and seniors.
Co-Director

Software (GitHub)

gnina
Deep learning for molecular docking

pharmit
Interactive exploration of chemical space

3Dmol.js
Molecular visualization with WebGL

qsar-tools
Collection of scripts for creating and visualizing 2D QSAR models

smina*
Scoring and Minimization with AutoDock Vina

AnchorQuery*
Specialized pharmacophore search for targeting protein-protein interactions with multicomponent reaction chemistry.

Pharmer*
General pharmacophore search open-source software.

ZINCPharmer*
Free online pharmacophore search engine for the ZINC database.

PocketQuery*
Identify PPI inhibitor starting points from PPI structure.

ShapeDB*
Indexed search of molecular shapes

*Developed in collaboration with the Camacho Lab

Funding

I am currently funded through R01GM108340 from the National Institute of General Medical Sciences. I have previously received funding through the Samuel and Emma Winters Foundation, the CTSI Biomedical Modeling Pilot Award, and aigrant.org, as well as hardware and software support from NVIDIA and Google Cloud Platform.

PittProxy: