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Items: 30

1.

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy.

Giordano-Attianese G, Gainza P, Gray-Gaillard E, Cribioli E, Shui S, Kim S, Kwak MJ, Vollers S, Corria Osorio AJ, Reichenbach P, Bonet J, Oh BH, Irving M, Coukos G, Correia BE.

Nat Biotechnol. 2020 Feb 3. doi: 10.1038/s41587-019-0403-9. [Epub ahead of print]

PMID:
32015549
2.

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.

Gainza P, Sverrisson F, Monti F, Rodolà E, Boscaini D, Bronstein MM, Correia BE.

Nat Methods. 2020 Feb;17(2):184-192. doi: 10.1038/s41592-019-0666-6. Epub 2019 Dec 9.

PMID:
31819266
3.

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics.

Bonet J, Harteveld Z, Sesterhenn F, Scheck A, Correia BE.

BMC Bioinformatics. 2019 May 15;20(1):240. doi: 10.1186/s12859-019-2796-3.

4.

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen.

Sesterhenn F, Galloux M, Vollers SS, Csepregi L, Yang C, Descamps D, Bonet J, Friedensohn S, Gainza P, Corthésy P, Chen M, Rosset S, Rameix-Welti MA, Éléouët JF, Reddy ST, Graham BS, Riffault S, Correia BE.

PLoS Biol. 2019 Feb 21;17(2):e3000164. doi: 10.1371/journal.pbio.3000164. eCollection 2019 Feb.

5.

Rosetta FunFolDes - A general framework for the computational design of functional proteins.

Bonet J, Wehrle S, Schriever K, Yang C, Billet A, Sesterhenn F, Scheck A, Sverrisson F, Veselkova B, Vollers S, Lourman R, Villard M, Rosset S, Krey T, Correia BE.

PLoS Comput Biol. 2018 Nov 19;14(11):e1006623. doi: 10.1371/journal.pcbi.1006623. eCollection 2018 Nov.

6.

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9.

Bubeck F, Hoffmann MD, Harteveld Z, Aschenbrenner S, Bietz A, Waldhauer MC, Börner K, Fakhiri J, Schmelas C, Dietz L, Grimm D, Correia BE, Eils R, Niopek D.

Nat Methods. 2018 Nov;15(11):924-927. doi: 10.1038/s41592-018-0178-9. Epub 2018 Oct 30.

PMID:
30377362
7.

Structure-based immunogen design-leading the way to the new age of precision vaccines.

Sesterhenn F, Bonet J, Correia BE.

Curr Opin Struct Biol. 2018 Aug;51:163-169. doi: 10.1016/j.sbi.2018.06.002. Epub 2018 Jun 29. Review.

PMID:
29980105
8.

Computational protein design-the next generation tool to expand synthetic biology applications.

Gainza-Cirauqui P, Correia BE.

Curr Opin Biotechnol. 2018 Aug;52:145-152. doi: 10.1016/j.copbio.2018.04.001. Epub 2018 May 2. Review.

PMID:
29729544
9.

Global profiling of lysine reactivity and ligandability in the human proteome.

Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF.

Nat Chem. 2017 Dec;9(12):1181-1190. doi: 10.1038/nchem.2826. Epub 2017 Jul 31.

10.

PRN473, an inhibitor of Bruton's tyrosine kinase, inhibits neutrophil recruitment via inhibition of macrophage antigen-1 signalling.

Herter JM, Margraf A, Volmering S, Correia BE, Bradshaw JM, Bisconte A, Hill RJ, Langrish CL, Lowell CA, Zarbock A.

Br J Pharmacol. 2018 Feb;175(3):429-439. doi: 10.1111/bph.14090. Epub 2017 Dec 22.

11.

Chemoproteomic profiling and discovery of protein electrophiles in human cells.

Matthews ML, He L, Horning BD, Olson EJ, Correia BE, Yates JR 3rd, Dawson PE, Cravatt BF.

Nat Chem. 2017 Mar;9(3):234-243. doi: 10.1038/nchem.2645. Epub 2016 Oct 31.

12.

Ligand and Target Discovery by Fragment-Based Screening in Human Cells.

Parker CG, Galmozzi A, Wang Y, Correia BE, Sasaki K, Joslyn CM, Kim AS, Cavallaro CL, Lawrence RM, Johnson SR, Narvaiza I, Saez E, Cravatt BF.

Cell. 2017 Jan 26;168(3):527-541.e29. doi: 10.1016/j.cell.2016.12.029. Epub 2017 Jan 19.

13.

Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.

Mousa JJ, Sauer MF, Sevy AM, Finn JA, Bates JT, Alvarado G, King HG, Loerinc LB, Fong RH, Doranz BJ, Correia BE, Kalyuzhniy O, Wen X, Jardetzky TS, Schief WR, Ohi MD, Meiler J, Crowe JE Jr.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6849-E6858. Epub 2016 Oct 17.

14.

Proteome-wide covalent ligand discovery in native biological systems.

Backus KM, Correia BE, Lum KM, Forli S, Horning BD, González-Páez GE, Chatterjee S, Lanning BR, Teijaro JR, Olson AJ, Wolan DW, Cravatt BF.

Nature. 2016 Jun 23;534(7608):570-4. doi: 10.1038/nature18002. Epub 2016 Jun 15.

15.

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

Sarti E, Gladich I, Zamuner S, Correia BE, Laio A.

Proteins. 2016 Sep;84(9):1312-20. doi: 10.1002/prot.25079. Epub 2016 Jun 23.

PMID:
27253756
16.

Motif-Driven Design of Protein-Protein Interfaces.

Silva DA, Correia BE, Procko E.

Methods Mol Biol. 2016;1414:285-304. doi: 10.1007/978-1-4939-3569-7_17.

PMID:
27094298
17.

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering.

Blackburn MC, Petrova E, Correia BE, Maerkl SJ.

Nucleic Acids Res. 2016 Apr 20;44(7):e68. doi: 10.1093/nar/gkv1497. Epub 2015 Dec 23.

18.

A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells.

Niphakis MJ, Lum KM, Cognetta AB 3rd, Correia BE, Ichu TA, Olucha J, Brown SJ, Kundu S, Piscitelli F, Rosen H, Cravatt BF.

Cell. 2015 Jun 18;161(7):1668-80. doi: 10.1016/j.cell.2015.05.045.

19.

Mapping the protein interaction landscape for fully functionalized small-molecule probes in human cells.

Kambe T, Correia BE, Niphakis MJ, Cravatt BF.

J Am Chem Soc. 2014 Jul 30;136(30):10777-82. doi: 10.1021/ja505517t. Epub 2014 Jul 21.

20.

A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells.

Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D.

Cell. 2014 Jun 19;157(7):1644-1656. doi: 10.1016/j.cell.2014.04.034.

21.

Proof of principle for epitope-focused vaccine design.

Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V, Connell MJ, Stevens E, Schroeter A, Chen M, Macpherson S, Serra AM, Adachi Y, Holmes MA, Li Y, Klevit RE, Graham BS, Wyatt RT, Baker D, Strong RK, Crowe JE Jr, Johnson PR, Schief WR.

Nature. 2014 Mar 13;507(7491):201-6. doi: 10.1038/nature12966. Epub 2014 Feb 5.

22.

Reversion of somatic mutations of the respiratory syncytial virus-specific human monoclonal antibody Fab19 reveal a direct relationship between association rate and neutralizing potency.

Bates JT, Keefer CJ, Utley TJ, Correia BE, Schief WR, Crowe JE Jr.

J Immunol. 2013 Apr 1;190(7):3732-9. doi: 10.4049/jimmunol.1202964. Epub 2013 Mar 1.

23.

Deciphering the molecular details for the binding of the prion protein to main ganglioside GM1 of neuronal membranes.

Sanghera N, Correia BE, Correia JR, Ludwig C, Agarwal S, Nakamura HK, Kuwata K, Samain E, Gill AC, Bonev BB, Pinheiro TJ.

Chem Biol. 2011 Nov 23;18(11):1422-31. doi: 10.1016/j.chembiol.2011.08.016.

24.

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.

Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR.

Science. 2011 Oct 21;334(6054):373-6. doi: 10.1126/science.1209368.

25.

High-resolution structure prediction of a circular permutation loop.

Correia BE, Holmes MA, Huang PS, Strong RK, Schief WR.

Protein Sci. 2011 Nov;20(11):1929-34. doi: 10.1002/pro.725. Epub 2011 Sep 30.

26.

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.

Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE.

Nature. 2011 Aug 21;477(7362):111-4. doi: 10.1038/nature10349.

27.

Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus.

McLellan JS, Correia BE, Chen M, Yang Y, Graham BS, Schief WR, Kwong PD.

J Mol Biol. 2011 Jun 24;409(5):853-66. doi: 10.1016/j.jmb.2011.04.044. Epub 2011 Apr 27.

28.

Computational protein design using flexible backbone remodeling and resurfacing: case studies in structure-based antigen design.

Correia BE, Ban YE, Friend DJ, Ellingson K, Xu H, Boni E, Bradley-Hewitt T, Bruhn-Johannsen JF, Stamatatos L, Strong RK, Schief WR.

J Mol Biol. 2011 Jan 7;405(1):284-97. doi: 10.1016/j.jmb.2010.09.061. Epub 2010 Oct 20.

PMID:
20969873
29.

Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.

Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather DN, Zenobia C, Burke KY, Bradley-Hewitt T, Bruhn-Johannsen JF, Kalyuzhniy O, Baker D, Strong RK, Stamatatos L, Schief WR.

Structure. 2010 Sep 8;18(9):1116-26. doi: 10.1016/j.str.2010.06.010.

30.

A structural model of an amyloid protofilament of transthyretin.

Correia BE, Loureiro-Ferreira N, Rodrigues JR, Brito RM.

Protein Sci. 2006 Jan;15(1):28-32. Epub 2005 Dec 1.

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