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Items: 1 to 50 of 52

1.

Leveraging a Low-Affinity Diazaspiro Orthosteric Fragment to Reduce Dopamine D3 Receptor (D3R) Ligand Promiscuity across Highly Conserved Aminergic G-Protein-Coupled Receptors (GPCRs).

Reilly SW, Riad AA, Hsieh CJ, Sahlholm K, Jacome DA, Griffin S, Taylor M, Weng CC, Xu K, Kirschner N, Luedtke RR, Parry C, Malhotra S, Karanicolas J, Mach RH.

J Med Chem. 2019 May 23;62(10):5132-5147. doi: 10.1021/acs.jmedchem.9b00412. Epub 2019 May 6.

PMID:
31021617
2.

Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream.

Van Tyne D, Manson AL, Huycke MM, Karanicolas J, Earl AM, Gilmore MS.

Sci Transl Med. 2019 Apr 10;11(487). pii: eaat8418. doi: 10.1126/scitranslmed.aat8418.

PMID:
30971455
3.

Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities.

Bai N, Roder H, Dickson A, Karanicolas J.

Sci Rep. 2019 Feb 25;9(1):2650. doi: 10.1038/s41598-018-37072-x.

4.

Allostery in Its Many Disguises: From Theory to Applications.

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, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.

PMID:
30744993
5.

Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer.

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.

Cell. 2018 Nov 15;175(5):1244-1258.e26. doi: 10.1016/j.cell.2018.09.051. Epub 2018 Oct 25.

PMID:
30454645
6.

Constructing Kinetically Controlled Denaturation Isotherms of Folded Proteins Using Denaturant-Pulse Chaperonin Binding.

O'Neil PT, Machen AJ, Thompson JA, Wang W, Hoang QQ, Baldwin MR, Khar KR, Karanicolas J, Fisher MT.

Methods Mol Biol. 2019;1873:293-304. doi: 10.1007/978-1-4939-8820-4_19.

PMID:
30341618
7.

Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity.

Rudolph MJ, Vance DJ, Kelow S, Angalakurthi SK, Nguyen S, Davis SA, Rong Y, Middaugh CR, Weis DD, Dunbrack R Jr, Karanicolas J, Mantis NJ.

Protein Eng Des Sel. 2018 Jul 1;31(7-8):277-287. doi: 10.1093/protein/gzy022.

PMID:
30265352
8.

Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins.

Lan L, Liu H, Smith AR, Appelman C, Yu J, Larsen S, Marquez RT, Wu X, Liu FY, Gao P, Gowthaman R, Karanicolas J, De Guzman RN, Rogers S, Aubé J, Neufeld KL, Xu L.

BMC Cancer. 2018 Aug 10;18(1):809. doi: 10.1186/s12885-018-4704-z.

9.

Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue.

Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J.

ACS Synth Biol. 2018 Apr 20;7(4):1152-1162. doi: 10.1021/acssynbio.8b00124. Epub 2018 Apr 9.

10.

Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase.

Keohane CE, Steele AD, Fetzer C, Khowsathit J, Van Tyne D, Moynié L, Gilmore MS, Karanicolas J, Sieber SA, Wuest WM.

J Am Chem Soc. 2018 Feb 7;140(5):1774-1782. doi: 10.1021/jacs.7b11212. Epub 2018 Jan 24.

11.

Identification of novel small molecule Beclin 1 mimetics activating autophagy.

Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aubé J, Sun B, Xu L.

Oncotarget. 2017 May 18;8(31):51355-51369. doi: 10.18632/oncotarget.17977. eCollection 2017 Aug 1.

12.

Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies.

Bazzoli A, Vance DJ, Rudolph MJ, Rong Y, Angalakurthi SK, Toth RT 4th, Middaugh CR, Volkin DB, Weis DD, Karanicolas J, Mantis NJ.

Proteins. 2017 Nov;85(11):1994-2008. doi: 10.1002/prot.25353. Epub 2017 Aug 4.

13.

Correction to When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

Malhotra S, Karanicolas J.

J Med Chem. 2017 Jul 13;60(13):5940. doi: 10.1021/acs.jmedchem.7b00868. Epub 2017 Jun 27. No abstract available.

PMID:
28653841
14.

Computational Screening and Design for Compounds that Disrupt Protein-protein Interactions.

Johnson DK, Karanicolas J.

Curr Top Med Chem. 2017;17(23):2703-2714. doi: 10.2174/1568026617666170508153904. Review.

PMID:
28482793
15.

The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.

Kaur K, Wu X, Fields JK, Johnson DK, Lan L, Pratt M, Somoza AD, Wang CCC, Karanicolas J, Oakley BR, Xu L, De Guzman RN.

PLoS One. 2017 Apr 17;12(4):e0175471. doi: 10.1371/journal.pone.0175471. eCollection 2017.

16.

"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.

Bazzoli A, Karanicolas J.

J Comput Chem. 2017 Jun 15;38(16):1321-1331. doi: 10.1002/jcc.24740. Epub 2017 Mar 20.

17.

Musashi RNA-Binding Proteins as Cancer Drivers and Novel Therapeutic Targets.

Kudinov AE, Karanicolas J, Golemis EA, Boumber Y.

Clin Cancer Res. 2017 May 1;23(9):2143-2153. doi: 10.1158/1078-0432.CCR-16-2728. Epub 2017 Jan 31. Review.

18.

When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

Malhotra S, Karanicolas J.

J Med Chem. 2017 Jan 12;60(1):128-145. doi: 10.1021/acs.jmedchem.6b00725. Epub 2016 Dec 16. Erratum in: J Med Chem. 2017 Jul 13;60(13):5940.

19.

Optimal allosteric stabilization sites using contact stabilization analysis.

Dickson A, Bailey CT, Karanicolas J.

J Comput Chem. 2017 Jun 5;38(15):1138-1146. doi: 10.1002/jcc.24517. Epub 2016 Oct 24.

20.

Chaperonin-Based Biolayer Interferometry To Assess the Kinetic Stability of Metastable, Aggregation-Prone Proteins.

Lea WA, O'Neil PT, Machen AJ, Naik S, Chaudhri T, McGinn-Straub W, Tischer A, Auton MT, Burns JR, Baldwin MR, Khar KR, Karanicolas J, Fisher MT.

Biochemistry. 2016 Sep 6;55(35):4885-908. doi: 10.1021/acs.biochem.6b00293. Epub 2016 Aug 19.

21.

Full and Partial Agonism of a Designed Enzyme Switch.

Budiardjo SJ, Licknack TJ, Cory MB, Kapros D, Roy A, Lovell S, Douglas J, Karanicolas J.

ACS Synth Biol. 2016 Dec 16;5(12):1475-1484. Epub 2016 Jul 22.

22.

Novel Ricin Subunit Antigens With Enhanced Capacity to Elicit Toxin-Neutralizing Antibody Responses in Mice.

Wahome N, Sully E, Singer C, Thomas JC, Hu L, Joshi SB, Volkin DB, Fang J, Karanicolas J, Jacobs DJ, Mantis NJ, Middaugh CR.

J Pharm Sci. 2016 May;105(5):1603-1613. doi: 10.1016/j.xphs.2016.02.009. Epub 2016 Mar 15.

23.

Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions.

Johnson DK, Karanicolas J.

J Chem Inf Model. 2016 Feb 22;56(2):399-411. doi: 10.1021/acs.jcim.5b00572. Epub 2016 Jan 14.

24.

Optogenetic Inhibitor of the Transcription Factor CREB.

Ali AM, Reis JM, Xia Y, Rashid AJ, Mercaldo V, Walters BJ, Brechun KE, Borisenko V, Josselyn SA, Karanicolas J, Woolley GA.

Chem Biol. 2015 Nov 19;22(11):1531-1539. doi: 10.1016/j.chembiol.2015.09.018.

25.

Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions.

Bazzoli A, Kelow SP, Karanicolas J.

PLoS One. 2015 Oct 20;10(10):e0140359. doi: 10.1371/journal.pone.0140359. eCollection 2015.

26.

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites.

Gowthaman R, Lyskov S, Karanicolas J.

PLoS One. 2015 Jul 16;10(7):e0131612. doi: 10.1371/journal.pone.0131612. eCollection 2015.

27.

DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.

Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J.

J Med Chem. 2016 May 12;59(9):4152-70. doi: 10.1021/acs.jmedchem.5b00150. Epub 2015 Jul 10.

28.

Natural product (-)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1.

Lan L, Appelman C, Smith AR, Yu J, Larsen S, Marquez RT, Liu H, Wu X, Gao P, Roy A, Anbanandam A, Gowthaman R, Karanicolas J, De Guzman RN, Rogers S, Aubé J, Ji M, Cohen RS, Neufeld KL, Xu L.

Mol Oncol. 2015 Aug;9(7):1406-20. doi: 10.1016/j.molonc.2015.03.014. Epub 2015 Apr 10.

29.

Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations.

Johnson DK, Karanicolas J.

PLoS Comput Biol. 2015 Feb 23;11(2):e1004081. doi: 10.1371/journal.pcbi.1004081. eCollection 2015 Feb.

30.

The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.

Xia Y, DiPrimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J.

J Am Chem Soc. 2013 Dec 18;135(50):18840-9. doi: 10.1021/ja407644b. Epub 2013 Dec 6.

31.

Fast docking on graphics processing units via Ray-Casting.

Khar KR, Goldschmidt L, Karanicolas J.

PLoS One. 2013 Aug 16;8(8):e70661. doi: 10.1371/journal.pone.0070661. eCollection 2013.

32.

Structural properties of non-traditional drug targets present new challenges for virtual screening.

Gowthaman R, Deeds EJ, Karanicolas J.

J Chem Inf Model. 2013 Aug 26;53(8):2073-81. doi: 10.1021/ci4002316. Epub 2013 Aug 13.

33.

Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin A chain subunit vaccine antigen.

Thomas JC, O'Hara JM, Hu L, Gao FP, Joshi SB, Volkin DB, Brey RN, Fang J, Karanicolas J, Mantis NJ, Middaugh CR.

Hum Vaccin Immunother. 2013 Apr;9(4):744-52. doi: 10.4161/hv.22998. Epub 2013 Apr 1.

34.

Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.

Johnson DK, Karanicolas J.

PLoS Comput Biol. 2013;9(3):e1002951. doi: 10.1371/journal.pcbi.1002951. Epub 2013 Mar 7.

35.

Designing allosteric control into enzymes by chemical rescue of structure.

Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J.

J Am Chem Soc. 2012 Jun 20;134(24):10055-60. doi: 10.1021/ja301409g. Epub 2012 Jun 11.

36.

Designing orthogonal signaling pathways: how to fit in with the surroundings.

Karanicolas J.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5140-1. doi: 10.1073/pnas.1202624109. Epub 2012 Mar 26. No abstract available.

37.

Hotspot-centric de novo design of protein binders.

Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D.

J Mol Biol. 2011 Nov 11;413(5):1047-62. doi: 10.1016/j.jmb.2011.09.001. Epub 2011 Sep 10.

38.

A phosphoarginine containing peptide as an artificial SH2 ligand.

Hofmann FT, Lindemann C, Salia H, Adamitzki P, Karanicolas J, Seebeck FP.

Chem Commun (Camb). 2011 Oct 7;47(37):10335-7. doi: 10.1039/c1cc13341a. Epub 2011 Aug 19.

PMID:
21853174
39.

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.

Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D.

Nature. 2011 Jun 15;475(7354):96-100. doi: 10.1038/nature10154.

40.

A de novo protein binding pair by computational design and directed evolution.

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.

Mol Cell. 2011 Apr 22;42(2):250-60. doi: 10.1016/j.molcel.2011.03.010. Epub 2011 Mar 31.

41.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

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, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.

Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6.

42.

Atomic accuracy in predicting and designing noncanonical RNA structure.

Das R, Karanicolas J, Baker D.

Nat Methods. 2010 Apr;7(4):291-4. doi: 10.1038/nmeth.1433. Epub 2010 Feb 28.

43.

Computational design of affinity and specificity at protein-protein interfaces.

Karanicolas J, Kuhlman B.

Curr Opin Struct Biol. 2009 Aug;19(4):458-63. doi: 10.1016/j.sbi.2009.07.005. Epub 2009 Jul 29. Review.

44.

Rationally designed integrin beta3 mutants stabilized in the high affinity conformation.

Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA.

J Biol Chem. 2009 Feb 6;284(6):3917-24. doi: 10.1074/jbc.M806312200. Epub 2008 Nov 19.

45.

The 3D profile method for identifying fibril-forming segments of proteins.

Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D.

Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4074-8. Epub 2006 Mar 7.

46.

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

Feig M, Karanicolas J, Brooks CL 3rd.

J Mol Graph Model. 2004 May;22(5):377-95.

PMID:
15099834
47.

Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain.

Karanicolas J, Brooks CL 3rd.

Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3432-7. Epub 2004 Feb 23.

48.
49.
50.

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

Karanicolas J, Brooks CL 3rd.

Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3954-9. Epub 2003 Mar 24.

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