☰

David R. Koes, Ph.D. - Publications

Affiliations: 
2009 Carnegie Mellon University, Pittsburgh, PA 
Area:
Computer Science
Tree Info Similar researchers PubMed Report error

29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Francoeur PG, Masuda T, Sunseri J, Jia A, Iovanisci RB, Snyder I, Koes DR. Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. Journal of Chemical Information and Modeling. PMID 32865404 DOI: 10.1021/Acs.Jcim.0C00411  0.337
2020 Sunseri J, Koes DR. libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. Journal of Chemical Information and Modeling. PMID 32049525 DOI: 10.1021/Acs.Jcim.9B01145  0.31
2019 McDermott L, Koes D, Mohammed S, Iyer P, Boby M, Balasubramanian V, Geedy M, Katt W, Cerione R. GAC inhibitors with a 4-hydroxypiperidine spacer: Requirements for potency. Bioorganic & Medicinal Chemistry Letters. 126632. PMID 31474484 DOI: 10.1016/J.Bmcl.2019.126632  0.313
2019 Chen L, Cruz A, Ramsey S, Dickson CJ, Duca JS, Hornak V, Koes DR, Kurtzman T. Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. Plos One. 14: e0220113. PMID 31430292 DOI: 10.1371/Journal.Pone.0220113  0.338
2018 Sunseri J, King JE, Francoeur PG, Koes DR. Convolutional neural network scoring and minimization in the D3R 2017 community challenge. Journal of Computer-Aided Molecular Design. PMID 29992528 DOI: 10.1007/S10822-018-0133-Y  0.323
2018 Hochuli J, Helbling A, Skaist T, Ragoza M, Koes DR. Visualizing convolutional neural network protein-ligand scoring. Journal of Molecular Graphics & Modelling. 84: 96-108. PMID 29940506 DOI: 10.1016/J.Jmgm.2018.06.005  0.303
2017 Gau D, Lewis T, Mcdermott L, Wipf P, Koes D, Roy P. Structure-based virtual screening identifies small molecule inhibitor of the profilin1-actin interaction. The Journal of Biological Chemistry. PMID 29282288 DOI: 10.1074/Jbc.M117.809137  0.318
2017 Koes DR, Dömling A, Camacho CJ. AnchorQuery: Rapid online virtual screening for small-molecule protein-protein interaction inhibitors. Protein Science : a Publication of the Protein Society. PMID 28921842 DOI: 10.1002/Pro.3303  0.369
2017 Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, ... Koes DR, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science : a Publication of the Protein Society. PMID 28836357 DOI: 10.1002/Pro.3280  0.322
2017 Ragoza M, Hochuli J, Idrobo E, Sunseri J, Koes DR. Protein–Ligand Scoring with Convolutional Neural Networks Journal of Chemical Information and Modeling. 57: 942-957. PMID 28368587 DOI: 10.1021/Acs.Jcim.6B00740  0.341
2016 Sunseri J, Ragoza M, Collins J, Koes DR. A D3R prospective evaluation of machine learning for protein-ligand scoring. Journal of Computer-Aided Molecular Design. PMID 27592011 DOI: 10.1007/S10822-016-9960-X  0.334
2016 Sunseri J, Koes DR. Pharmit: Interactive Exploration of Chemical Space Nucleic Acids Research. 44. PMID 27095195 DOI: 10.1093/Nar/Gkw287  0.351
2016 Hain E, Camacho CJ, Koes DR. Fragment oriented molecular shapes. Journal of Molecular Graphics & Modelling. 66: 143-154. PMID 27085751 DOI: 10.1016/J.Jmgm.2016.03.017  0.348
2015 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. 10: e0134697. PMID 26258606 DOI: 10.1371/Journal.Pone.0134697  0.377
2015 Koes DR, Camacho CJ. Indexing Volumetric Shapes with Matching and Packing. Knowledge and Information Systems. 43: 157-180. PMID 26085707 DOI: 10.1007/S10115-014-0729-Z  0.32
2015 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. PMID 26001785 DOI: 10.1074/Jbc.M114.629964  0.309
2015 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. 10: 490-7. PMID 25677305 DOI: 10.1002/Cmdc.201500028  0.307
2015 Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics (Oxford, England). 31: 1322-4. PMID 25505090 DOI: 10.1093/Bioinformatics/Btu829  0.313
2014 Koes DR, Camacho CJ. Shape-based virtual screening with volumetric aligned molecular shapes. Journal of Computational Chemistry. 35: 1824-34. PMID 25049193 DOI: 10.1002/Jcc.23690  0.358
2014 Rahaman MM, Reinders F, Watkins CE, Nguyen A, Miller MP, Koes D, Gladwin MT, Camacho CJ, Straub AC. Novel Small Molecule Inhibitors of Cytochrome B5 Reductase 3 Were Identified by Structure Guided Chemical Modifications of Propylthiouracil Free Radical Biology and Medicine. 76: S89-S90. DOI: 10.1016/J.Freeradbiomed.2014.10.312  0.304
2013 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. 53: 1893-904. PMID 23379370 DOI: 10.1021/Ci300604Z  0.308
2012 Koes DR, Camacho CJ. ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Research. 40: W409-14. PMID 22553363 DOI: 10.1093/Nar/Gks378  0.33
2012 Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Research. 40: W387-92. PMID 22523085 DOI: 10.1093/Nar/Gks336  0.328
2012 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. 7: e32839. PMID 22427896 DOI: 10.1371/Journal.Pone.0032839  0.385
2012 Koes DR, Camacho CJ. Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics (Oxford, England). 28: 784-91. PMID 22210869 DOI: 10.1093/Bioinformatics/Btr717  0.336
2011 Koes DR, Camacho CJ. Pharmer: efficient and exact pharmacophore search. Journal of Chemical Information and Modeling. 51: 1307-14. PMID 21604800 DOI: 10.1021/Ci200097M  0.383
2009 Koes DR, Goldstein SC. Register allocation deconstructed Acm International Conference Proceeding Series. 320: 21-30.  0.547
2008 Koes DR, Goldstein SC. Near-optimal instruction selection on DAGs Proceedings of the 2008 Cgo - Sixth International Symposium On Code Generation and Optimization. 45-54. DOI: 10.1145/1356058.1356065  0.551
2006 Koes DR, Goldstein SC. A global progressive register allocator Acm Sigplan Notices. 41: 204-215. DOI: 10.1145/1133255.1134006  0.549
Show low-probability matches.