recent publications
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academic article
- Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Behar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., et al. Allostery in its many disguises: from theory to applications Structure 2019 27:566-578 DOI:10.1016/j.str.2019.01.003 PMID:30744993
- Van Tyne, D., Manson, A. L., Huycke, M. M., Karanicolas, J., Earl, A. M., Gilmore, M. S. Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream Science Translational Medicine 2019 11 DOI:10.1126/scitranslmed.aat8418 PMID:30971455
- Bai, N., Roder, H., Dickson, A., Karanicolas, J. Isothermal analysis of ThermoFluor Data can readily provide quantitative binding affinities Scientific Reports 2019 9 DOI:10.1038/s41598-018-37072-x PMID:30804351 PMCID:PMC6389909
- Reilly, S. W., Riad, A. A., Hsieh, C. J., Sahlholm, K., Jacome, D. A., Griffin, S., Taylor, M., Weng, C. C., Xu, K., Kirschner, N., Luedtke, R. R., Parry, C., et al. Leveraging a low-affinity diazaspiro orthosteric fragment to reduce dopamine D3 receptor (D3R) ligand promiscuity across highly conserved aminergic G-protein-coupled receptors (GPCRs) Journal of Medicinal Chemistry 2019 62:5132-5147 DOI:10.1021/acs.jmedchem.9b00412 PMID:31021617
- Rudolph, M. J., Vance, D. J., Kelow, S., Angalakurthi, S. K., Nguyen, S., Davis, S. A., Rong, Y., Middaugh, C. R., Weis, D. D., Dunbrack Jr., R., Karanicolas, J., Mantis, N. J. Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity Protein Engineering Design & Selection 2018 31:277-287 DOI:10.1093/protein/gzy022 PMID:30265352 PMCID:PMC6277176
- Kaiser, C. E., Pabon, J. P. R., Khowsathit, J., Castaldi, M. P., Kazmirski, S. L., Weis, D. D., Zhang, A. X., Karanicolas, J. Modulating antibody structure and function through directed mutations and chemical rescue ACS Synthetic Biology 2018 7:1152-1162 DOI:10.1021/acssynbio.8b00124 PMID:29609459 PMCID:PMC5910032
- Lan, L., Liu, H., Smith, A. R., Appelman, C., Yu, J., Larsen, S., Marquez, R. T., Wu, X., Liu, F. Y., Gao, P., Gowthaman, R., Karanicolas, J., et al. Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins BMC Cancer 2018 18 DOI:10.1186/s12885-018-4704-z PMID:30097032 PMCID:PMC6086024
- Keohane, C. E., Steele, A. D., Fetzer, C., Khowsathit, J., Van Tyne, D., Maynie, L., Gilmore, M. S., Karanicolas, J., Sieber, S. A., Wuest, W. M. Promysalin elicits species-selective inhibition of pseudomonas aeruginosa by targeting succinate dehydrogenase Journal of the American Chemical Society 2018 140:1774-1782 DOI:10.1021/jacs.7b11212 PMID:29300464 PMCID:PMC5869686
- Zhang, H., Pandey, S., Travers, M., Sun, H., Morton, G., Madzo, J., Chung, W., Khowsathit, J., Perez-Leal, O., Barrero, C. A., Merali, C., Okamoto, Y., et al. Targeting CDK9 reactivates epigenetically silenced genes in cancer Cell 2018 175:1244-1258 DOI:10.1016/j.cell.2018.09.051 PMID:30454645 PMCID:PMC6247954
- Bazzoli, A., Karanicolas, J. "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics Journal of Computational Chemistry 2017 38:1321-1331 DOI:10.1002/jcc.24740 PMID:28318014 PMCID:PMC5407913
- Johnson, D. K., Karanicolas, J. Computational screening and design for compounds that disrupt protein-protein interactions Current Topics in Medicinal Chemistry 2017 17:2703-2714 DOI:10.2174/1568026617666170508153904 PMID:28482793
- Yu, J., Lan, L., Lewin, S. J., Rogers, S. A., Roy, A., Wu, X., Gao, P., Karanicolas, J., Aube, J., Sun, B., Xu, L. Identification of novel small molecule Beclin 1 mimetics activating autophagy Oncotarget 2017 8:51355-51369 DOI:10.18632/oncotarget.17977 PMID:28881653 PMCID:PMC5584254
- Kudinov, A. E., Karanicolas, J., Golemis, E. A., Boumber, Y. Musashi RNA-binding proteins as cancer drivers and novel therapeutic targets Clinical Cancer Research 2017 23:2143-2153 DOI:10.1158/1078-0432.ccr-16-2728 PMID:28143872 PMCID:PMC5413399
- Dickson, A., Bailey, C. T., Karanicolas, J. Optimal allosteric stabilization sites using contact stabilization analysis Journal of Computational Chemistry 2017 38:1138-1146 DOI:10.1002/jcc.24517 PMID:27774625 PMCID:PMC5403592
- Kaur, K., Wu, X., Fields, J. K., Johnson, D. K., Lan, L., Pratt, M., Somoza, A. D., Wang, C. C. C., Karanicolas, J., Oakley, B. R., Xu, L., De Guzman, R. N. The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro PLoS One 2017 12 DOI:10.1371/journal.pone.0175471 PMID:28414767 PMCID:PMC5393604
- Bazzoli, A., Vance, D. J., Rudolph, M. J., Rong, Y. H., Angalakurthi, S. K., Toth, R. T., Middaugh, C. R., Volkin, D. B., Weis, D. D., Karanicolas, J., Mantis, N. J. Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies Proteins-Structure Function and Bioinformatics 2017 85:1994-2008 DOI:10.1002/prot.25353 PMID:28718923 PMCID:PMC5754017
- Malhotra, S., Karanicolas, J. When does chemical elaboration induce a ligand to change its binding mode? Journal of Medicinal Chemistry 2017 60:128-145 DOI:10.1021/acs.jmedchem.6b00725 PMID:27982595 PMCID:PMC5525026
- Lea, W. A., O'Neil, P. T., Machen, A. J., Naik, S., Chaudhri, T., McGinn-Straub, W., Tischer, A., Auton, M. T., Burns, J. R., Baldwin, M. R., Khar, K. R., Karanicolas, J., et al. Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins Biochemistry 2016 55:4885-4908 DOI:10.1021/acs.biochem.6b00293 PMID:27505032
- Gowthaman, R., Miller, S. A., Rogers, S., Khowsathit, J., Lan, L., Bai, N., Johnson, D. K., Liu, C., Xu, L., Anbanandam, A., Aube, J., Roy, A., et al. DARC: Mapping surface topography by ray-casting for effective virtual screening at protein interaction sites Journal of Medicinal Chemistry 2016 59:4152-4170 DOI:10.1021/acs.jmedchem.5b00150 PMID:26126123 PMCID:PMC4707132
- Budiardjo, S. J., Licknack, T. J., Cory, M. B., Kapros, D., Roy, A., Lovell, S., Douglas, J., Karanicolas, J. Full and partial agonism of a designed enzyme switch ACS Synthetic Biology 2016 5:1475-1484 DOI:10.1021/acssynbio.6b00097 PMID:27389009 PMCID:PMC5161622
- Wahome, N., Sully, E., Singer, C., Thomas, J. C., Hu, L., Joshi, S. B., Volkin, D. B., Fang, J. W., Karanicolas, J., Jacobs, D. J., Mantis, N. J., Middaugh, C. R. Novel ricin subunit antigens with enhanced capacity to elicit toxin-neutralizing antibody responses in mice Journal of Pharmaceutical Sciences 2016 105:1603-1613 DOI:10.1016/j.xphs.2016.02.009 PMID:26987947 PMCID:PMC4846473
- Johnson, D. K., Karanicolas, J. Ultra-high-throughput structure-based virtual screening for small molecule inhibitors of protein-protein interactions Journal of Chemical Information and Modeling 2016 56:399-411 DOI:10.1021/acs.jcim.5b00572 PMID:26726827 PMCID:PMC4765363
- Gowthaman, R., Lyskov, S., Karanicolas, J. DARC 2.0: Improved docking and virtual screening at protein interaction sites PLoS One 2015 10 DOI:10.1371/journal.pone.0131612 PMID:26181386 PMCID:PMC4504481
- Bazzoli, A., Kelow, S. P., Karanicolas, J. Enhancements to the Rosetta energy function enable improved identification of small molecules that inhibit protein-protein interactions PLoS One 2015 10 DOI:10.1371/journal.pone.0140359 PMID:26484863 PMCID:PMC4617380
- Lan, L., Appelman, C., Smith, A. R., Yu, J., Larsen, S., Marquez, R. T., Liu, H., Wu, X., Gao, P., Roy, A., Anbanandam, A., Gowthaman, R., et al. Natural product (-)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1 Molecular Oncology 2015 9:1406-1420 DOI:10.1016/j.molonc.2015.03.014 PMID:25933687 PMCID:PMC4523432
- Ali, A. M., Reis, J. M., Xia, Y., Rashid, A. J., Mercaldo, V., Walters, B. J., Brechun, K. E., Borisenko, V., Josselyn, S. A., Karanicolas, J., Woolley, G. A. Optogenetic inhibitor of the transcription factor CREB Chemistry & Biology 2015 22:1531-1539 DOI:10.1016/j.chembiol.2015.09.018 PMID:26590638 PMCID:PMC4656143
- Johnson, D. K., Karanicolas, J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations PLoS Computational Biology 2015 11 DOI:10.1371/journal.pcbi.1004081 PMID:25706586 PMCID:PMC4338137
- Johnson, D. K., Karanicolas, J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface PLoS Computational Biology 2013 9 DOI:10.1371/journal.pcbi.1002951 PMID:23505360 PMCID:PMC3591273
- Thomas, J. C., O'Hara, J. M., Hu, L., Gao, F. P., Joshi, S. B., Volkin, D. B., Brey, R. N., Fang, J., Karanicolas, J., Mantis, N. J., Middaugh, C. R. Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin A chain subunit vaccine antigen Human Vaccines & Immunotherapeutics 2013 9:744-752 DOI:10.4161/hv.22998 PMID:23563512 PMCID:PMC3903890
- Khar, K. R., Goldschmidt, L., Karanicolas, J. Fast docking on graphics processing units via Ray-Casting PLoS One 2013 8 DOI:10.1371/journal.pone.0070661 PMID:23976948 PMCID:PMC3745428
- Gowthaman, R., Deeds, E. J., Karanicolas, J. Structural properties of non-traditional drug targets present new challenges for virtual screening Journal of Chemical Information and Modeling 2013 53:2073-2081 DOI:10.1021/ci4002316 PMID:23879197 PMCID:PMC3819422
- Xia, Y., DiPrimio, N., Keppel, T. R., Vo, B., Fraser, K., Battaiei, K. P., Egan, C., Bystroff, C., Lovell, S., Weis, D. D., Anderson, J. C., Karanicolas, J. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation Journal of the American Chemical Society 2013 135:18840-18849 DOI:10.1021/ja407644b PMID:24313858 PMCID:PMC3919134
- Deckert, K., Budiardjo, S. J., Brunner, L. C., Lovell, S., Karanicolas, J. Designing allosteric control into enzymes by chemical rescue of structure Journal of the American Chemical Society 2012 134:10055-10060 DOI:10.1021/ja301409g PMID:22655749 PMCID:PMC3381609
- 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 2012 109:5140-5141 DOI:10.1073/pnas.1202624109 PMID:22451928 PMCID:PMC3325707
- Karanicolas, J., Com, J. E., Chen, I., Joachimiak, L. A., Dym, O., Peck, S. H., Albeck, S., Unger, T., Hu, W., Liu, G., Delbecq, S., Montelione, G. T., et al. A de novo protein binding pair by computational design and directed evolution Molecular Cell 2011 42:250-260 DOI:10.1016/j.molcel.2011.03.010 PMID:21458342 PMCID:PMC3102007
- Hofmann, F. T., Lindemann, C., Salia, H., Adamitzki, P., Karanicolas, J., Seebeck, F. P. A phosphoarginine containing peptide as an artificial SH2 ligand Chemical Communications 2011 47:10335-10337 DOI:10.1039/c1cc13341a PMID:21853174
- Fleishman, S. J., Corn, J. E., Strauch, E. M., Whitehead, T. A., Karanicolas, J., Baker, D. Hotspot-centric de novo design of protein binders Journal of Molecular Biology 2011 413:1047-1062 DOI:10.1016/j.jmb.2011.09.001 PMID:21945116 PMCID:PMC4144197
- Leaver-Fay, A., Tyka, M., Lewis, S. M., Lange, O. F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P. D., Smith, C. A., Sheffler, W., Davis, I. W., Cooper, S., et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules Methods in Enzymology 2011 545-574 DOI:10.1016/s0076-6879(11)87019-9 PMID:21187238 PMCID:PMC4083816
- Sievers, S. A., Karanicolas, J., Chang, H. W., Zhao, A., Jiang, L., Zirafi, O., Stevens, J. T., Munch, J., Baker, D., Eisenberg, D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation Nature 2011 475:96-100 DOI:10.1038/nature10154 PMID:21677644 PMCID:PMC4073670
- Das, R., Karanicolas, J., Baker, D. Atomic accuracy in predicting and designing noncanonical RNA structure Nature Methods 2010 7:291-294 DOI:10.1038/nmeth.1433 PMID:20190761 PMCID:PMC2854559
- Karanicolas, J., Kuhlman, B. Computational design of affinity and specificity at protein-protein interfaces Current Opinion in Structural Biology 2009 19:458-463 DOI:10.1016/j.sbi.2009.07.005 PMID:19646858 PMCID:PMC2882636
- Luo, B. H., Karanicolas, J., Harmacek, L. D., Baker, D., Springer, T. A. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal of Biological Chemistry 2009 284:3917-3924 DOI:10.1074/jbc.M806312200
- Thompson, M. J., Sievers, S. A., Karanicolas, J., Ivanova, M. I., 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 2006 103:4074-4078 DOI:10.1073/pnas.0511295103 PMID:16537487 PMCID:PMC1449648
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Karanicolas, J., Brooks III, C. L.
An evolution of minimalist models for protein folding: from the behavior of protein-like polymers to protein function
Drug Discovery Today: BIOSILICO
2004
2:127-133
DOI:10.1016/S1741-8364(04)02404-7
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Karanicolas, J., Brooks III, C. L.
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
2004
101:3432-3437
DOI:10.1073/pnas.0304825101
PMID:14981252
PMCID:PMC373479
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Feig, M., Karanicolas, J., Brooks III, C. L.
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
Journal of Molecular Graphics & Modelling
2004
22:377-395
DOI:10.1016/j.jmgm.2003.12.005
PMID:15099834
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Karanicolas, J., Brooks III, C. L.
Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions
Journal of Molecular Biology
2003
334:309-325
DOI:10.1016/j.jmb.2003.09.047
PMID:14607121
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Karanicolas, J., Brooks III, C. L.
The importance of explicit chain representation in protein folding models: an examination of Ising-like models
Proteins-Structure Function and Genetics
2003
53:740-747
DOI:10.1002/prot.10459
PMID:14579364
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Karanicolas, J., Brooks III, C. L.
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
2003
100:3954-3959
DOI:10.1073/pnas.0731771100
PMID:12655041
PMCID:PMC153029
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Karanicolas, J., Brooks III, C. L.
The origins of asymmetry in the folding transition states of protein L and protein G
Protein Science
2002
11:2351-2361
DOI:10.1110/ps.0205402
PMID:12237457
PMCID:PMC2373711
- Karanicolas, J., Fu, S., Power, J. F. Depth profiling the thermal reflection coefficient of an opaque solid via an inverse thermal wave scattering theory based on the Method of Images Applied Physics B-Lasers and Optics 2000 71:217-223
- Power, J. F., Karanicolas, J., Fu, S. Method of Images direct mapping of one-dimensional heat flow patterns in an arbitrarily layered solid Applied Physics B-Lasers and Optics 2000 71:57-67
- Liu, D., Karanicolas, J., Yu, C., Zhang, Z., Woolley, G. A. Site-specific incorporation of photoisomerizable azobenzene groups into ribonuclease S Bioorganic & Medicinal Chemistry Letters 1997 7:2677-2680 DOI:10.1016/s0960-894x(97)10044-0
- Woolley, G. A., Zunic, V., Karanicolas, J., Jaikaran, A. S. I., Starostin, A. V. Voltage-dependent behavior of a ''ball-and-chain'' gramicidin channel Biophysical Journal 1997 73:2465-2475 PMID:9370440 PMCID:PMC1181148