Full list available here

◆ Kirubakaran P*, Morton G*, Zhang P*, Zhang H, Gordon J, Abou-Gharbia M, Issa JPJ, Wu J, Childers W†, Karanicolas J†. “Comparative modeling of CDK9 inhibitors to explore selectivity and structure-activity relationships” bioRxiv.

◆ Malhotra S, Karanicolas J. “A numerical transform of random forest regressors corrects systematically-biased predictions” arXiv.

◆ Bai N, Miller SA, Andrianov GV, Yates M, Kirubakaran P, Karanicolas J. "Rationalizing PROTAC-mediated ternary complex formation using Rosetta" J. Chem. Inf. Model., 61, p. 1368-1382 (2021).

◆ Adeshina YO, Deeds EJ, Karanicolas J. "Machine learning classification can reduce false positives in structure-based virtual screening" PNAS, 117, p. 18477-18488 (2020).

◆ Khowsathit J, Bazzoli A, Cheng H, Karanicolas J. "Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation" ACS Cent. Sci., 6, p. 390-403 (2020).

◆ Zhang H, Pandey S, Travers M, Sun H, Morton G, Madzo J, Chung W, Khowsathit J, Perez-Leal O, Barrero CA, Merali C, Okamoto Y, Sato T, Pan J, Garriga J, Bhanu NV, Simithy J, Patel B, Huang J, Raynal NJ, Garcia BA, Jacobson MA, Kadoch C, Merali S, Zhang Y, Childers W, Abou-Gharbia M, Karanicolas J, Baylin SB, Zahnow CA, Jelinek J, Graña X, Issa JJ. “Targeting CDK9 reactivates epigenetically silenced genes in cancer” Cell, 175, p. 1244-1258 (2018).

◆ Malhotra S, Karanicolas J. “When does chemical elaboration induce a ligand to change its binding mode?” J. Med. Chem., 60, p. 128-45 (2017).

◆ Johnson DK, Karanicolas J. “Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions” J. Chem. Inf. Model., 56, p. 399-411 (2016).

◆ Gowthaman R*, Miller S*, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J. “DARC: mapping surface topography by ray-casting for effective virtual screening at protein interaction sites” J. Med. Chem., 59, p. 4152-70 (2016).

◆ Johnson DK, Karanicolas J. “Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations” PLOS Comput. Biol., 11, p. e1004081 (2015).

◆ Xia Y, DiPrimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J. “The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation” J. Amer. Chem. Soc., 135, p. 18840-9  (2013).

◆ Johnson DK, Karanicolas J. “Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface” PLOS Comput. Biol., 9, p. e1002951 (2013).

◆ Deckert K, Budiardjo SJ, Brunner LC, Lovell S, and Karanicolas J. “Designing allosteric control into enzymes by chemical rescue of structure” J. Amer. Chem. Soc., 134, p. 10055-60  (2012).

* equally contributing co-authors † co-corresponding authors