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Items: 10

1.

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. 2019 Dec 9. doi: 10.1038/s41592-019-0666-6. [Epub ahead of print]

PMID:
31819266
2.

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.

3.

OSPREY 3.0: Open-source protein redesign for you, with powerful new features.

Hallen MA, Martin JW, Ojewole A, Jou JD, Lowegard AU, Frenkel MS, Gainza P, Nisonoff HM, Mukund A, Wang S, Holt GT, Zhou D, Dowd E, Donald BR.

J Comput Chem. 2018 Nov 15;39(30):2494-2507. doi: 10.1002/jcc.25522. Epub 2018 Oct 14.

4.

OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design.

Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, Anderson AC, Donald BR.

Methods Mol Biol. 2017;1529:291-306.

5.

Algorithms for protein design.

Gainza P, Nisonoff HM, Donald BR.

Curr Opin Struct Biol. 2016 Aug;39:16-26. doi: 10.1016/j.sbi.2016.03.006. Epub 2016 Apr 14. Review.

6.

Fast gap-free enumeration of conformations and sequences for protein design.

Roberts KE, Gainza P, Hallen MA, Donald BR.

Proteins. 2015 Oct;83(10):1859-1877. doi: 10.1002/prot.24870. Epub 2015 Aug 24.

7.

Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design.

Hallen MA, Gainza P, Donald BR.

J Chem Theory Comput. 2015 May 12;11(5):2292-306.

8.

Protein design algorithms predict viable resistance to an experimental antifolate.

Reeve SM, Gainza P, Frey KM, Georgiev I, Donald BR, Anderson AC.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):749-54. doi: 10.1073/pnas.1411548112. Epub 2014 Dec 31.

9.

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR.

Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9.

10.

Protein design using continuous rotamers.

Gainza P, Roberts KE, Donald BR.

PLoS Comput Biol. 2012 Jan;8(1):e1002335. doi: 10.1371/journal.pcbi.1002335. Epub 2012 Jan 12.

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