Contact Information
BST3 Suite 3064
3501 Fifth Avenue
Pittsburgh, PA, 15260
Phone: (412) 383-5745
David Koes 
Primary Appointment: 
Assistant Professor, Computational and Systems Biology, School of Medicine, University of Pittsburgh
Peer-reviewed Publications:
Current Research/Scholarship
My research is to develop novel computational algorithms and build full-scale systems to support rapid and inexpensive drug discovery. I have created the first scalable algorithms for performing pharmacophore and molecular shape search of large databases of chemical compounds. I am actively investigating novel learning algorithms for empirical scoring function development and the role of molecular dynamics in binding affinity prediction. We've built several systems that enable online drug discovery, including PocketQuery, AnchorQuery, ZINCPharmer, smina, 3Dmol.js, and Pharmit.
Research/Scholarship Interests
algorithms; bioinformatics; computational biology; computational drug discovery; molecular modeling; protein-protein interactions; virtual screening
(Legend: Current Major/ Current Minor, Non-current Major/ Non-current Minor )

Education & Training
PostDocComputational BiologyUniversity of Pittsburgh
MSComputer ScienceCarnegie Mellon University in 2006
PhDComputer ScienceCarnegie Mellon University in 2009
BSComputer ScienceCarnegie Mellon University in 2001

Selected Publications
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Sunseri J, Koes DR. Pharmit: interactive exploration of chemical space. Nucleic Acids Research. 2016 Jul 8;44(W1):W442-8. PMID:27095195. doi:10.1093/nar/gkw287.
Hain E, Camacho CJ, Koes DR. Fragment oriented molecular shapes. Journal of Molecular Graphics & Modelling. 2016 May;66:143-54. PMID:27085751. PMCID:PMC4862882. doi:10.1016/j.jmgm.2016.03.017.
Marani M, Paone A, Fiascarelli A, Macone A, Gargano M, Rinaldo S, Giardina G, Pontecorvi V, Koes D, McDermott L, Yang T, Paiardini A, Contestabile R, Cutruzzolà F. A pyrazolopyran derivative preferentially inhibits the activity of human cytosolic serine hydroxymethyltransferase and induces cell death in lung cancer cells. Oncotarget. 2016 Jan 26;7(4):4570-83. PMID:26717037. PMCID:PMC4826227. doi:10.18632/oncotarget.6726.
Gau D, Veon W, Zeng X, Yates N, Shroff SG, Koes DR, Roy P. Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A. PloS One. 2016;11(5):e0156313. PMID:27228149. PMCID:PMC4882052. doi:10.1371/journal.pone.0156313.
Rahaman MM, Reinders FG, Koes D, Nguyen AT, Mutchler SM, Sparacino-Watkins C, Alvarez RA, Miller MP, Cheng D, Chen BB, Jackson EK, Camacho CJ, Straub AC. Structure Guided Chemical Modifications of Propylthiouracil Reveal Novel Small Molecule Inhibitors of Cytochrome b5 Reductase 3 That Increase Nitric Oxide Bioavailability. The Journal of Biological Chemistry. 2015 Jul 3;290(27):16861-72. PMID:26001785. PMCID:PMC4505432. doi:10.1074/jbc.M114.629964.
Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics (Oxford, England). 2015 Apr 15;31(8):1322-4. PMID:25505090. PMCID:PMC4393526. doi:10.1093/bioinformatics/btu829.
Koes DR, Camacho CJ. Indexing Volumetric Shapes with Matching and Packing. Knowledge and Information Systems. 2015 Apr 1;43(1):157-180. PMID:26085707. PMCID:PMC4465823. doi:10.1007/s10115-014-0729-z.
Paiardini A, Fiascarelli A, Rinaldo S, Daidone F, Giardina G, Koes DR, Parroni A, Montini G, Marani M, Paone A, McDermott LA, Contestabile R, Cutruzzolà F. Screening and in vitro testing of antifolate inhibitors of human cytosolic serine hydroxymethyltransferase. ChemMedChem. 2015 Mar;10(3):490-7. PMID:25677305. doi:10.1002/cmdc.201500028.
Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. PloS One. 2015;10(8):e0134697. PMID:26258606. PMCID:PMC4530941. doi:10.1371/journal.pone.0134697.
Koes D. Pharmacophore Modeling: Methods and Applications. In: Methods in Pharmacology and Toxicology. Humana Press; 2015.. doi: (Invited)
Koes DR, Camacho CJ. Shape-based virtual screening with volumetric aligned molecular shapes. Journal of Computational Chemistry. 2014 Sep 30;35(25):1824-34. PMID:25049193. PMCID:PMC4140985. doi:10.1002/jcc.23690.
Luciani T, Wenskovitch J, Chen K, Koes D, Travers T, Marai GE. FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families. BMC Proceedings. 2014;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S3. PMID:25237390. PMCID:PMC4155608. doi:10.1186/1753-6561-8-S2-S3.
Koes DR, Baumgartner MP, Camacho CJ. Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. Journal of Chemical Information and Modeling. 2013 Aug 26;53(8):1893-904. PMID:23379370. PMCID:PMC3726561. doi:10.1021/ci300604z.
Koes D, Camacho CJ, Doemling AS. Interactive Technologies for Leveraging the Known Chemistry of Anchor Residues to Disrupt Protein Interactions. In: Doemling AS, Mannhold R, Kubinyi H, Folkers G, editors. Protein-Protein Interactions in Drug Discovery. Wiley; 2013 Mar.
Koes DR, Camacho CJ. ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Research. 2012 Jul;40(Web Server issue):W409-14. PMID:22553363. PMCID:PMC3394271. doi:10.1093/nar/gks378.
Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Research. 2012 Jul;40(Web Server issue):W387-92. PMID:22523085. PMCID:PMC3394328. doi:10.1093/nar/gks336.
Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics (Oxford, England). 2012 Mar 15;28(6):784-91. PMID:22210869. PMCID:PMC3307105. doi:10.1093/bioinformatics/btr717.
Huang Y, Wolf S, Koes D, Popowicz GM, Camacho CJ, Holak TA, Dömling A. Exhaustive fluorine scanning toward potent p53-Mdm2 antagonists. ChemMedChem. 2012 Jan 2;7(1):49-52. PMID:21954050. PMCID:PMC3772510. doi:10.1002/cmdc.201100428.
Koes D, Khoury K, Huang Y, Wang W, Bista M, Popowicz GM, Wolf S, Holak TA, Dömling A, Camacho CJ. Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PloS One. 2012;7(3):e32839. PMID:22427896. PMCID:PMC3299697. doi:10.1371/journal.pone.0032839.
Koes DR, Camacho CJ. Pharmer: efficient and exact pharmacophore search. Journal of Chemical Information and Modeling. 2011 Jun 27;51(6):1307-14. PMID:21604800. PMCID:PMC3124593. doi:10.1021/ci200097m.
Koes D, Goldstein SC. Register Allocation Deconstructed. In: Proceedings of the 12th International Workshop on Software and Compilers for Embedded Systems. SCOPES 09; Nice, France. New York: ACM; 2009. 21-30.
Koes D, Goldstein SC. Near-Optimal Instruction Selection on DAGs. In: Proceedings of the 6th Annual IEEE/ACM International Symposium on Code Generation and Optimization. CGO '08; Boston, MA. New York: ACM; 2008. 45-54.
David Ryan Koes and Seth Copen Goldstein. "An Analysis of Graph Coloring Register Allocation," Carnegie Mellon University Technical Report No. CMU-CS-06-111. March, 2006
Koes D, Goldstein SC. A Global Progressive Register Allocator. In: Proceedings of the 2006 ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI '06; 2006; Ottawa. New York: ACM; 2006. 204-215.
Koes D, Goldstein SC. A Progressive Register Allocator for Irregular Architectures. In: Proceedings of the International Symposium on Code Generation and Optimization. CGO '05; San Jose, CA. Washington, DC: IEEE Computer Society; 2005. 269-280.
David Ryan Koes, Tiberiu Chelcea, Charles Onyeama, and Seth Copen Goldstein. "Adding Faster with Application Specific Early Termination," Carnegie Mellon University Technical Report No. CMU-CS-05-101. May, 2005
Koes D, Budiu M, Venkataramani G, Goldstein SC. Programmer Specified Pointer Independence. In: Proceedings of the 2004 Workshop on Memory System Performance. MSP '04; Washington, DC. New York, NY: ACM; 2004. 51-59.
Strelow D, Mishler J, Koes D, Singh S. Precise omnidirectional camera calibration. IEEE Computer Vision and Pattern Recognition. 2001.