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John Karanicolas - Publications

Affiliations: 
2008-2016 University of Kansas, Lawrence, KS, United States 
 2016- Fox Chase Cancer Center 
Website:
https://www.foxchase.org/john-karanicolas
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43 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 Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, et al. Identification and Validation of an Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers. 12. PMID 32784494 DOI: 10.3390/Cancers12082221  0.301
2020 Adeshina YO, Deeds EJ, Karanicolas J. Machine learning classification can reduce false positives in structure-based virtual screening. Proceedings of the National Academy of Sciences of the United States of America. PMID 32669436 DOI: 10.1073/Pnas.2000585117  0.308
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Karanicolas J, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.576
2020 Post SJ, Keohane CE, Rossiter LM, Kaplan AR, Khowsathit J, Matuska K, Karanicolas J, Wuest WM. Target-Based Design of Promysalin Analogues Identifies a New Putative Binding Cleft in Succinate Dehydrogenase. Acs Infectious Diseases. PMID 32286041 DOI: 10.1021/Acsinfecdis.0C00024  0.379
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 Central Science. 6: 390-403. PMID 32232139 DOI: 10.1021/Acscentsci.9B01065  0.328
2019 Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Scientific Reports. 9: 2650. PMID 30804351 DOI: 10.1038/S41598-018-37072-X  0.58
2019 Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003  0.333
2019 O'Neil PT, Machen AJ, Thompson JA, Wang W, Hoang QQ, Baldwin MR, Khar KR, Karanicolas J, Fisher MT. Constructing Kinetically Controlled Denaturation Isotherms of Folded Proteins Using Denaturant-Pulse Chaperonin Binding. Methods in Molecular Biology (Clifton, N.J.). 1873: 293-304. PMID 30341618 DOI: 10.1007/978-1-4939-8820-4_19  0.361
2017 Bazzoli A, Vance DJ, Rudolph MJ, Rong Y, Angalakurthi SK, Toth RT, Middaugh CR, Volkin DB, Weis DD, Karanicolas J, Mantis NJ. Using Homology Modeling to Interrogate Binding Affinity in Neutralization of Ricin Toxin by a Family of Single Domain Antibodies. Proteins. PMID 28718923 DOI: 10.1002/Prot.25353  0.305
2017 Johnson DK, Karanicolas J. Computational screening and design for compounds that disrupt protein-protein interactions. Current Topics in Medicinal Chemistry. PMID 28482793 DOI: 10.2174/1568026617666170508153904  0.408
2017 Bazzoli A, Karanicolas J. "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. Journal of Computational Chemistry. PMID 28318014 DOI: 10.1002/Jcc.24740  0.312
2017 Boumber Y, Kudinov AE, Karanicolas J, Golemis EA. Musashi RNA-binding proteins as cancer drivers and novel therapeutic targets. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28143872 DOI: 10.1158/1078-0432.Ccr-16-2728  0.324
2017 Lan L, Smith A, Wu X, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Oakley B, Guzman RD, Neufeld K, Xu L. Abstract 1133: Discovery of novel small molecule inhibitors of RNA-binding protein Musashi-1 Cancer Research. 77: 1133-1133. DOI: 10.1158/1538-7445.Am2017-1133  0.301
2016 Dickson A, Bailey CT, Karanicolas J. Optimal allosteric stabilization sites using contact stabilization analysis. Journal of Computational Chemistry. PMID 27774625 DOI: 10.1002/Jcc.24517  0.563
2016 Lea WA, O 'Neil PT, Machen AJ, Naik S, Chaudhuri TK, McGinn-Straub W, Tischer A, Auton MT, Burns JR, Baldwin MR, Khar KR, Karanicolas J, Fisher MT. Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins. Biochemistry. PMID 27505032 DOI: 10.1021/Acs.Biochem.6B00293  0.361
2016 Budiardjo SJ, Licknack TJ, Cory MB, Kapros D, Roy A, Lovell SW, Douglas JT, Karanicolas J. Full and Partial Agonism of a Designed Enzyme Switch. Acs Synthetic Biology. PMID 27389009 DOI: 10.1021/Acssynbio.6B00097  0.767
2016 Johnson DK, Karanicolas J. Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions. Journal of Chemical Information and Modeling. PMID 26726827 DOI: 10.1021/Acs.Jcim.5B00572  0.4
2015 Bazzoli A, Kelow SP, Karanicolas J. Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions. Plos One. 10: e0140359. PMID 26484863 DOI: 10.1371/Journal.Pone.0140359  0.377
2015 Gowthaman R, Lyskov S, Karanicolas J. DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites. Plos One. 10: e0131612. PMID 26181386 DOI: 10.1371/Journal.Pone.0131612  0.418
2015 Gowthaman R, Miller SA, Rogers SA, 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. Journal of Medicinal Chemistry. PMID 26126123 DOI: 10.1021/Acs.Jmedchem.5B00150  0.394
2015 Johnson DK, Karanicolas J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations. Plos Computational Biology. 11: e1004081. PMID 25706586 DOI: 10.1371/Journal.Pcbi.1004081  0.36
2013 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. Journal of the American Chemical Society. 135: 18840-9. PMID 24313858 DOI: 10.1021/Ja407644B  0.692
2013 Khar KR, Goldschmidt L, Karanicolas J. Fast docking on graphics processing units via Ray-Casting. Plos One. 8: e70661. PMID 23976948 DOI: 10.1371/Journal.Pone.0070661  0.307
2013 Gowthaman R, Deeds EJ, Karanicolas J. Structural properties of non-traditional drug targets present new challenges for virtual screening. Journal of Chemical Information and Modeling. 53: 2073-81. PMID 23879197 DOI: 10.1021/Ci4002316  0.388
2013 Thomas JC, O'Hara JM, Hu L, Gao FP, Joshi SB, Volkin DB, Brey RN, Fang J, Karanicolas J, Mantis NJ, Middaugh CR. Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin A chain subunit vaccine antigen. Human Vaccines & Immunotherapeutics. 9: 744-52. PMID 23563512 DOI: 10.4161/Hv.22998  0.303
2013 Johnson DK, Karanicolas J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. Plos Computational Biology. 9: e1002951. PMID 23505360 DOI: 10.1371/Journal.Pcbi.1002951  0.396
2012 Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J. Designing allosteric control into enzymes by chemical rescue of structure. Journal of the American Chemical Society. 134: 10055-60. PMID 22655749 DOI: 10.1021/Ja301409G  0.736
2012 Karanicolas J. Designing orthogonal signaling pathways: how to fit in with the surroundings. Proceedings of the National Academy of Sciences of the United States of America. 109: 5140-1. PMID 22451928 DOI: 10.1073/Pnas.1202624109  0.324
2011 Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D. Hotspot-centric de novo design of protein binders. Journal of Molecular Biology. 413: 1047-62. PMID 21945116 DOI: 10.1016/J.Jmb.2011.09.001  0.774
2011 Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 475: 96-100. PMID 21677644 DOI: 10.1038/Nature10154  0.513
2011 Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR, Baker D. A de novo protein binding pair by computational design and directed evolution. Molecular Cell. 42: 250-60. PMID 21458342 DOI: 10.1016/J.Molcel.2011.03.010  0.746
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Karanicolas J, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  0.689
2010 Das R, Karanicolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods. 7: 291-4. PMID 20190761 DOI: 10.1038/Nmeth.1433  0.566
2009 Karanicolas J, Kuhlman B. Computational design of affinity and specificity at protein-protein interfaces. Current Opinion in Structural Biology. 19: 458-63. PMID 19646858 DOI: 10.1016/J.Sbi.2009.07.005  0.641
2009 Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of Biological Chemistry. 284: 3917-24. PMID 19019827 DOI: 10.1074/Jbc.M806312200  0.434
2006 Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 4074-8. PMID 16537487 DOI: 10.1073/Pnas.0511295103  0.397
2004 Feig M, Karanicolas J, Brooks CL. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics & Modelling. 22: 377-95. PMID 15099834 DOI: 10.1016/J.Jmgm.2003.12.005  0.683
2004 Karanicolas J, Brooks CL. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proceedings of the National Academy of Sciences of the United States of America. 101: 3432-7. PMID 14981252 DOI: 10.1073/Pnas.0304825101  0.495
2004 Karanicolas J, Brooks CL. An evolution of minimalist models for protein folding: From the behavior of protein-like polymers to protein function Drug Discovery Today: Biosilico. 2: 127-133. DOI: 10.1016/S1741-8364(04)02404-7  0.552
2003 Karanicolas J, Brooks CL. Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. Journal of Molecular Biology. 334: 309-25. PMID 14607121 DOI: 10.1016/J.Jmb.2003.09.047  0.535
2003 Karanicolas J, Brooks CL. The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins. 53: 740-7. PMID 14579364 DOI: 10.1002/Prot.10459  0.549
2003 Karanicolas J, Brooks CL. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proceedings of the National Academy of Sciences of the United States of America. 100: 3954-9. PMID 12655041 DOI: 10.1073/Pnas.0731771100  0.53
2002 Karanicolas J, Brooks CL. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Science : a Publication of the Protein Society. 11: 2351-61. PMID 12237457 DOI: 10.1110/Ps.0205402  0.493
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