COBB2035: Modern Methods for Structure Based Drug Discovery
An introduction to the modern computational approaches and governing physical and chemical principles that underpin structure-based drug discovery.
Fall Semester (2025–)
David Ryan Koes, PhD
I am an Associate Professor in the Department of Computational and Systems Biology at the University of Pittsburgh and Co-Director of the Carnegie Mellon – University of Pittsburgh Ph.D. Program in Computational Biology (CPCB). I am also affiliated with the Computational Biomedicine & Biotechnology (COBB) Master of Science program.
My research combines molecular modeling, algorithm design, and machine learning to make drug discovery better, faster and cheaper. I develop computational algorithms and practical software tools, and apply these methods towards the discovery of new therapeutics. I am committed to open-source software and open science.
Publications
People
PhD Students
- Rishal Aggarwal
- Emma Flynn
- Jacky Chen
- Fareeda Abu-Juam (co-advised)
- Ben Krummenacher (co-advised)
- Marios Gavrielatos
Other Graduate Students
- Paula Sharoubeem (COBB)
- Sihyun Park (CMU MSAS)
- Jiameng Song (COBB)
- Wenxin Zhang (CMU QuantBio MS)
- Chenyun Guan (CMU CompBio MS)
- Jordan Epstein (COBB)
Former Members
Former PhD Students
- Daniel Peñaherrera
- Ian Dunn
- Drew McNutt
- Jonathan King
- Paul Francoeur
- Jocelyn Sunseri
Former Other Graduate Students
- Liv Toft (CMU CompBio MS)
- Justin Shao (CMU CompBio MS)
- Sumeet Kothare (CMU CompBio MS)
- Juhi Gupta (CMU CompBio MS)
- Tyler Katz (CMU CompBio MS)
- Pratham Lotia (CMU Biotech MS)
- Yao Wang (COBB)
- Nate Odonkor (CMU CompBio MS)
- Andrew Lutsky (CMU QuantBio MS)
- Minhyek Jeon (CMU CompBio MS)
- Rosalie Nolen (PittMed)
- Vratin Srivastava (CMU CompBio MS)
- Zoey Yang (CMU CompBio MS)
- Yanjing Li (CMU CompBio MS)
- William Hsu (CMU CompBio MS)
- Sitong Liu (CMU CompBio MS)
- Jackie Vo (CMU CompBio MS)
- Dillon Gavlock (COBB)
Former Research Fellows and PostDocs
- Somayeh Pirhadi
- Dakota Folmsbee
- Matthew Ragoza
- Rishal Aggarwal
- Tomohide Masuda
Teaching
COBB2060: Machine Learning for Biomedical Applications
Successor to Scalable. Less distributed and cloud computing. The focus remains on applications rather than theory. Co-taught with Maria Chikina
Spring Semester (2025–)
Former Courses
MSCBIO2066: 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 Maria Chikina
Spring Semester (2016–2024)
MSCBIO2025: Introduction to Bioinformatics Programming in Python
A graduate-level introductory programming course with a focus on analyzing biological data.
Fall Semester (2013–2023)
MSCBIO2030: Introduction to Computational Structural Biology
An introduction into the physical, chemical, and algorithmic underpinnings of computational structural biology.
Fall 2022, Spring 2025
CompBio Academy (formerly DiscoBio)
The Computational Biology Summer Academy at UPMC Hillman Cancer Center.
An experiential summer academy for rising high school juniors and seniors.
Co-Director 2013–2023
Software
GitHub →gnina
Deep learning for molecular docking
pharmit
Interactive exploration of chemical space
3Dmol.js
Molecular visualization with WebGL
OMTRA
Multi-task generative model for structure-based drug discovery.
FlowMol3
Flow matching model for unconditional 3D de novo molecule generation.
libmolgrid
Python library for CUDA accelerated molecular gridding
SolTranNet
Molecule attention transformer for aqueous solubility prediction.
qsar-tools
Collection of scripts for creating and visualizing 2D QSAR models
smina*
Scoring and Minimization with AutoDock Vina
*Developed in collaboration with the Camacho Lab
Funding
I currently have no extramural funding :-(
I have previously received funding from R35GM140753 from the National Institute of General Medical Sciences, CHE-2102474 from the National Science Foundation (with Geoff Hutchison), R21EY032632 from the National Eye Institute (with Partha Roy, Donna Huryn, and Andrew VanDemark), R01GM108340 from the National Institute of General Medical Sciences, CHE-1800435 from the National Science Foundation (with Geoff Hutchison), R21NS107785 from the National Institute of Neurological Disorders and Stroke (with Sam Poloyac and Lee McDermott), Relay Therapeutics, 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.