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.

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

Software

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

Publications



PittProxy: