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Bai N,
Miller SA,
Andrianov GV,
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Karanicolas J. Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta.
J Chem Inf Model. 2021 Feb 24
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Ruggiero MJ,
Malhotra S,
Fenton AW,
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Karanicolas J,
Hagenbuch B. A clinically-relevant polymorphism in the Na(+)/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position.
J Biol Chem. 2020 Nov 9
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Lan L,
Liu J,
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Smith AR,
Wang J,
Wu X,
Appelman C,
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Karanicolas J,
Somoza AD,
Wang CCC,
Miao Y,
De Guzman R,
Oakley BR,
Neufeld KL,
Xu L. Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction.
Cancers (Basel). 2020 Aug 8;12(8)
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Adeshina YO,
Deeds EJ,
Karanicolas J. Machine learning classification can reduce false positives in structure-based virtual screening.
Proc Natl Acad Sci U S A. 2020 Aug 4;117(31)
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Leman JK,
Weitzner BD,
Lewis SM,
Adolf-Bryfogle J,
Alam N,
Alford RF,
Aprahamian M,
Baker D,
Barlow KA,
Barth P,
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Bender BJ,
Blacklock K,
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Boyken SE,
Bradley P,
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Conway P,
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Coventry B,
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Dunbrack R,
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Geniesse C,
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Gray JJ,
Gront D,
Guffy S,
Horowitz S,
Huang PS,
Huber T,
Jacobs TM,
Jeliazkov JR,
Johnson DK,
Kappel K,
Karanicolas J,
Khakzad H,
Khar KR,
Khare SD,
Khatib F,
Khramushin A,
King IC,
Kleffner R,
Koepnick B,
Kortemme T,
Kuenze G,
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Kuroda D,
Labonte JW,
Lai JK,
Lapidoth G,
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Lyskov S,
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Meiler J,
Moretti R,
Mulligan VK,
Nerli S,
Norn C,
O'Conchuir S,
Ollikainen N,
Ovchinnikov S,
Pacella MS,
Pan X,
Park H,
Pavlovicz RE,
Pethe M,
Pierce BG,
Pilla KB,
Raveh B,
Renfrew PD,
Burman SSR,
Rubenstein A,
Sauer MF,
Scheck A,
Schief W,
Schueler-Furman O,
Sedan Y,
Sevy AM,
Sgourakis NG,
Shi L,
Siegel JB,
Silva DA,
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Song Y,
Stein A,
Szegedy M,
Teets FD,
Thyme SB,
Wang RY,
Watkins A,
Zimmerman L,
Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Nat Methods. 2020 Jul;17(7)
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Wu X,
Gardashova G,
Lan L,
Han S,
Zhong C,
Marquez RT,
Wei L,
Wood S,
Roy S,
Gowthaman R,
Karanicolas J,
Gao FP,
Dixon DA,
Welch DR,
Li L,
Ji M,
Aube J,
Xu L. Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis.
Commun Biol. 2020 Apr 24;3(1)
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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 Infect Dis. 2020 Apr 14;6(6)
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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. 2020 Mar 25;6(3)
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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. Leveraging a Low-Affinity Diazaspiro Orthosteric Fragment to Reduce Dopamine D 3 Receptor (D 3 R) Ligand Promiscuity across Highly Conserved Aminergic G-Protein-Coupled Receptors (GPCRs).
J Med Chem. 2019 May 23;62(10)
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Van Tyne D,
Manson AL,
Huycke MM,
Karanicolas J,
Earl AM,
Gilmore MS. Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream.
Sci Transl Med. 2019 Apr 10;11(487)
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Wodak SJ,
Paci E,
Dokholyan NV,
Berezovsky IN,
Horovitz A,
Li J,
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Bahar I,
Karanicolas J,
Stock G,
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Stote RH,
Eberhardt J,
Chebaro Y,
Dejaegere A,
Cecchini M,
Changeux JP,
Bolhuis PG,
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Structure. 2019 Apr 2;27(4)
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Bai N,
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Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities.
Sci Rep. 2019 Feb 25;9(1)
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O'Neil PT,
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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 Mol Biol. 2019 ;1873
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Zhang H,
Pandey S,
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Sun H,
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Huang J,
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Garcia BA,
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Childers W,
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Baylin SB,
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Cell. 2018 Nov 15;175(5)
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Lan L,
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Appelman C,
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Larsen S,
Marquez RT,
Wu X,
Liu FY,
Gao P,
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De Guzman RN,
Rogers S,
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BMC Cancer. 2018 Aug 10;18(1)
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Rudolph MJ,
Vance DJ,
Kelow S,
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Nguyen S,
Davis SA,
Rong Y,
Middaugh CR,
Weis DD,
Dunbrack R Jr,
Karanicolas J,
Mantis NJ. Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity.
Protein Eng Des Sel. 2018 Jul 1;31(7-8)
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Kaiser CE,
Rincon Pabon JP,
Khowsathit J,
Castaldi MP,
Kazmirski SL,
Weis DD,
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Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue.
ACS Synth Biol. 2018 Apr 20;7(4)
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Keohane CE,
Steele AD,
Fetzer C,
Khowsathit J,
Van Tyne D,
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Sieber SA,
Wuest WM. Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase.
J Am Chem Soc. 2018 Feb 7;140(5)
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Bazzoli A,
Vance DJ,
Rudolph MJ,
Rong Y,
Angalakurthi SK,
Toth RTth,
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. 2017 Nov;85(11)
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Bazzoli A,
Karanicolas J. "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.
J Comput Chem. 2017 Jun 15;38(16)
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Dickson A,
Bailey CT,
Karanicolas J. Optimal allosteric stabilization sites using contact stabilization analysis.
J Comput Chem. 2017 Jun 05;38(15)
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Johnson DK,
Karanicolas J. Computational screening and design for compounds that disrupt protein-protein interactions.
Curr Top Med Chem. 2017 May 08;17(23)
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Kudinov AE,
Karanicolas J,
Golemis EA,
Boumber Y. Musashi RNA-binding proteins as cancer drivers and novel therapeutic targets.
Clin Cancer Res. 2017 May 01;23(9)
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Malhotra S,
Karanicolas J. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?.
J Med Chem. 2017 Jan 12;60(1)
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