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Defining the Kv2.1-syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant.

Yeh CY, Ye Z, Moutal A, Gaur S, Henton AM, Kouvaros S, Saloman JL, Hartnett-Scott KA, Tzounopoulos T, Khanna R, Aizenman E, Camacho CJ.

Proc Natl Acad Sci U S A. 2019 Jul 15. pii: 201903401. doi: 10.1073/pnas.1903401116. [Epub ahead of print]


NADPH oxidase 2 inhibitors CPP11G and CPP11H attenuate endothelial cell inflammation & vessel dysfunction and restore mouse hind-limb flow.

Li Y, Cifuentes-Pagano E, DeVallance ER, de Jesus DS, Sahoo S, Meijles DN, Koes D, Camacho CJ, Ross M, St Croix C, Pagano PJ.

Redox Biol. 2019 Apr;22:101143. doi: 10.1016/j.redox.2019.101143. Epub 2019 Feb 15.


A network-centric approach to drugging TNF-induced NF-κB signaling.

Pabon NA, Zhang Q, Cruz JA, Schipper DL, Camacho CJ, Lee REC.

Nat Commun. 2019 Feb 26;10(1):860. doi: 10.1038/s41467-019-08802-0.


Predicting protein targets for drug-like compounds using transcriptomics.

Pabon NA, Xia Y, Estabrooks SK, Ye Z, Herbrand AK, Süß E, Biondi RM, Assimon VA, Gestwicki JE, Brodsky JL, Camacho CJ, Bar-Joseph Z.

PLoS Comput Biol. 2018 Dec 7;14(12):e1006651. doi: 10.1371/journal.pcbi.1006651. eCollection 2018 Dec.


Electrophilic fatty acids impair RAD51 function and potentiate the effects of DNA-damaging agents on growth of triple-negative breast cells.

Asan A, Skoko JJ, Woodcock CC, Wingert BM, Woodcock SR, Normolle D, Huang Y, Stark JM, Camacho CJ, Freeman BA, Neumann CA.

J Biol Chem. 2019 Jan 11;294(2):397-404. doi: 10.1074/jbc.AC118.005899. Epub 2018 Nov 26.


A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription.

Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE.

J Biol Chem. 2018 Dec 28;293(52):19942-19956. doi: 10.1074/jbc.RA118.005627. Epub 2018 Oct 24.


Improving small molecule virtual screening strategies for the next generation of therapeutics.

Wingert BM, Camacho CJ.

Curr Opin Chem Biol. 2018 Jun;44:87-92. doi: 10.1016/j.cbpa.2018.06.006. Epub 2018 Jun 17. Review.


Case series: Pyramidal cataracts, intact irides and nystagmus from three novel PAX6 mutations.

Chauhan BK, Medsinge A, Baumgartner MP, Scanga HL, Kamakari S, Gajdosova E, Camacho CJ, Nischal KK.

Am J Ophthalmol Case Rep. 2018 Feb 28;10:172-179. doi: 10.1016/j.ajoc.2018.02.021. eCollection 2018 Jun.


AnchorQuery: Rapid online virtual screening for small-molecule protein-protein interaction inhibitors.

Koes DR, Dömling A, Camacho CJ.

Protein Sci. 2018 Jan;27(1):229-232. doi: 10.1002/pro.3303. Epub 2017 Oct 24.


Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.

Wingert BM, Oerlemans R, Camacho CJ.

J Comput Aided Mol Des. 2018 Jan;32(1):287-297. doi: 10.1007/s10822-017-0065-y. Epub 2017 Sep 16.


Symmetry breaking during homodimeric assembly activates an E3 ubiquitin ligase.

Ye Z, Needham PG, Estabrooks SK, Whitaker SK, Garcia BL, Misra S, Brodsky JL, Camacho CJ.

Sci Rep. 2017 May 11;7(1):1789. doi: 10.1038/s41598-017-01880-4.


Probing protein flexibility reveals a mechanism for selective promiscuity.

Pabon NA, Camacho CJ.

Elife. 2017 Apr 22;6. pii: e22889. doi: 10.7554/eLife.22889.


Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge.

Ye Z, Baumgartner MP, Wingert BM, Camacho CJ.

J Comput Aided Mol Des. 2016 Sep;30(9):695-706. Epub 2016 Aug 29.


Extensive Citrullination Promotes Immunogenicity of HSP90 through Protein Unfolding and Exposure of Cryptic Epitopes.

Travers TS, Harlow L, Rosas IO, Gochuico BR, Mikuls TR, Bhattacharya SK, Camacho CJ, Ascherman DP.

J Immunol. 2016 Sep 1;197(5):1926-36. doi: 10.4049/jimmunol.1600162. Epub 2016 Jul 22.


Fragment oriented molecular shapes.

Hain E, Camacho CJ, Koes DR.

J Mol Graph Model. 2016 May;66:143-54. doi: 10.1016/j.jmgm.2016.03.017. Epub 2016 Apr 2.


Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences.

Tejero J, Kapralov AA, Baumgartner MP, Sparacino-Watkins CE, Anthonymutu TS, Vlasova II, Camacho CJ, Gladwin MT, Bayir H, Kagan VE.

Biochim Biophys Acta. 2016 May;1861(5):391-401. doi: 10.1016/j.bbalip.2016.02.022. Epub 2016 Feb 27.


Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods.

Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A.

Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13933-6. doi: 10.1002/anie.201506310. Epub 2015 Sep 4.


Focusing on shared subpockets - new developments in fragment-based drug discovery.

Abdelraheem EM, Camacho CJ, Dömling A.

Expert Opin Drug Discov. 2015;10(11):1179-87. doi: 10.1517/17460441.2015.1080684. Epub 2015 Aug 21. Review.


A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool.

Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ.

PLoS One. 2015 Aug 10;10(8):e0134697. doi: 10.1371/journal.pone.0134697. eCollection 2015.


Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment.

Baumgartner MP, Camacho CJ.

J Chem Inf Model. 2016 Jun 27;56(6):1004-12. doi: 10.1021/acs.jcim.5b00338. Epub 2015 Aug 7.


Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE.

PLoS One. 2015 Jul 29;10(7):e0133590. doi: 10.1371/journal.pone.0133590. eCollection 2015.


Indexing Volumetric Shapes with Matching and Packing.

Koes DR, Camacho CJ.

Knowl Inf Syst. 2015 Apr 1;43(1):157-180.


Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function.

Travers T, Shao H, Joughin BA, Lauffenburger DA, Wells A, Camacho CJ.

Sci Signal. 2015 May 26;8(378):ra51. doi: 10.1126/scisignal.aaa1977.


Structure Guided Chemical Modifications of Propylthiouracil Reveal Novel Small Molecule Inhibitors of Cytochrome b5 Reductase 3 That Increase Nitric Oxide Bioavailability.

Rahaman MM, Reinders FG, Koes D, Nguyen AT, Mutchler SM, Sparacino-Watkins C, Alvarez RA, Miller MP, Cheng D, Chen BB, Jackson EK, Camacho CJ, Straub AC.

J Biol Chem. 2015 Jul 3;290(27):16861-72. doi: 10.1074/jbc.M114.629964. Epub 2015 May 22.


Restricted protein phosphatase 2A targeting by Merkel cell polyomavirus small T antigen.

Kwun HJ, Shuda M, Camacho CJ, Gamper AM, Thant M, Chang Y, Moore PS.

J Virol. 2015 Apr;89(8):4191-200. doi: 10.1128/JVI.00157-15. Epub 2015 Jan 28.


A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region.

Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE.

Chem Biol Drug Des. 2015 Aug;86(2):144-55. doi: 10.1111/cbdd.12473. Epub 2014 Nov 28.


Shape-based virtual screening with volumetric aligned molecular shapes.

Koes DR, Camacho CJ.

J Comput Chem. 2014 Sep 30;35(25):1824-34. doi: 10.1002/jcc.23690. Epub 2014 Jul 22.


Discovery of a novel activator of 5-lipoxygenase from an anacardic acid derived compound collection.

Wisastra R, Kok PA, Eleftheriadis N, Baumgartner MP, Camacho CJ, Haisma HJ, Dekker FJ.

Bioorg Med Chem. 2013 Dec 15;21(24):7763-78. doi: 10.1016/j.bmc.2013.10.015. Epub 2013 Oct 23.


Merkel cell polyomavirus small T antigen controls viral replication and oncoprotein expression by targeting the cellular ubiquitin ligase SCFFbw7.

Kwun HJ, Shuda M, Feng H, Camacho CJ, Moore PS, Chang Y.

Cell Host Microbe. 2013 Aug 14;14(2):125-35. doi: 10.1016/j.chom.2013.06.008.


The carboxyl tail of alpha-actinin-4 regulates its susceptibility to m-calpain and thus functions in cell migration and spreading.

Shao H, Travers T, Camacho CJ, Wells A.

Int J Biochem Cell Biol. 2013 Jun;45(6):1051-63. doi: 10.1016/j.biocel.2013.02.015. Epub 2013 Mar 1.


Modeling the assembly of the multiple domains of α-actinin-4 and its role in actin cross-linking.

Travers T, Shao H, Wells A, Camacho CJ.

Biophys J. 2013 Feb 5;104(3):705-15. doi: 10.1016/j.bpj.2012.12.003.


Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.

Koes DR, Baumgartner MP, Camacho CJ.

J Chem Inf Model. 2013 Aug 26;53(8):1893-904. doi: 10.1021/ci300604z. Epub 2013 Feb 12.


ZINCPharmer: pharmacophore search of the ZINC database.

Koes DR, Camacho CJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W409-14. doi: 10.1093/nar/gks378. Epub 2012 May 2.


PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure.

Koes DR, Camacho CJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W387-92. doi: 10.1093/nar/gks336. Epub 2012 Apr 20.


Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists.

Koes D, Khoury K, Huang Y, Wang W, Bista M, Popowicz GM, Wolf S, Holak TA, Dömling A, Camacho CJ.

PLoS One. 2012;7(3):e32839. doi: 10.1371/journal.pone.0032839. Epub 2012 Mar 12.


Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure.

Koes DR, Camacho CJ.

Bioinformatics. 2012 Mar 15;28(6):784-91. doi: 10.1093/bioinformatics/btr717. Epub 2011 Dec 30. Erratum in: Bioinformatics. 2012 Jul 15;28(14):1951.


Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D.

J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29.


Exhaustive fluorine scanning toward potent p53-Mdm2 antagonists.

Huang Y, Wolf S, Koes D, Popowicz GM, Camacho CJ, Holak TA, Dömling A.

ChemMedChem. 2012 Jan 2;7(1):49-52. doi: 10.1002/cmdc.201100428. Epub 2011 Sep 27. No abstract available.


Pharmer: efficient and exact pharmacophore search.

Koes DR, Camacho CJ.

J Chem Inf Model. 2011 Jun 27;51(6):1307-14. doi: 10.1021/ci200097m. Epub 2011 Jun 2.


Novel modulation factor quantifies the role of water molecules in protein interactions.

Bueno M, Temiz NA, Camacho CJ.

Proteins. 2010 Nov 15;78(15):3226-34. doi: 10.1002/prot.22805.


ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery.

Meireles LM, Dömling AS, Camacho CJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W407-11. doi: 10.1093/nar/gkq502. Epub 2010 Jun 4.


Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.

Temiz AN, Benos PV, Camacho CJ.

Nucleic Acids Res. 2010 Apr;38(7):2134-44. doi: 10.1093/nar/gkp1132. Epub 2010 Jan 4.


Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.

Temiz NA, Trapp A, Prokopyev OA, Camacho CJ.

Bioinformatics. 2010 Feb 1;26(3):319-25. doi: 10.1093/bioinformatics/btp664. Epub 2009 Dec 4.


Toward a quantitative theory of intrinsically disordered proteins and their function.

Liu J, Faeder JR, Camacho CJ.

Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19819-23. doi: 10.1073/pnas.0907710106. Epub 2009 Nov 10.


SUMOylation of nuclear actin.

Hofmann WA, Arduini A, Nicol SM, Camacho CJ, Lessard JL, Fuller-Pace FV, de Lanerolle P.

J Cell Biol. 2009 Jul 27;186(2):193-200. doi: 10.1083/jcb.200905016.


Structural and thermodynamic approach to peptide immunogenicity.

Camacho CJ, Katsumata Y, Ascherman DP.

PLoS Comput Biol. 2008 Nov;4(11):e1000231. doi: 10.1371/journal.pcbi.1000231. Epub 2008 Nov 21.


Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation.

Camacho CJ.

PLoS One. 2008 Oct 3;3(10):e3342. doi: 10.1371/journal.pone.0003342.


Species-specific immune responses generated by histidyl-tRNA synthetase immunization are associated with muscle and lung inflammation.

Katsumata Y, Ridgway WM, Oriss T, Gu X, Chin D, Wu Y, Fertig N, Oury T, Vandersteen D, Clemens P, Camacho CJ, Weinberg A, Ascherman DP.

J Autoimmun. 2007 Sep-Nov;29(2-3):174-86.

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