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Mining tertiary structural motifs for assessment of designability.
Zhang J, Grigoryan G. Zhang J, et al. Among authors: grigoryan g. Methods Enzymol. 2013;523:21-40. doi: 10.1016/B978-0-12-394292-0.00002-3. Methods Enzymol. 2013. PMID: 23422424 Free PMC article.
Absolute free energies of biomolecules from unperturbed ensembles.
Grigoryan G. Grigoryan G. J Comput Chem. 2013 Dec 5;34(31):2726-41. doi: 10.1002/jcc.23448. Epub 2013 Oct 16. J Comput Chem. 2013. PMID: 24132787
Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.
Frappier V, Jenson JM, Zhou J, Grigoryan G, Keating AE. Frappier V, et al. Among authors: grigoryan g. Structure. 2019 Apr 2;27(4):606-617.e5. doi: 10.1016/j.str.2019.01.008. Epub 2019 Feb 14. Structure. 2019. PMID: 30773399 Free PMC article.
De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.
Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, DeGrado WF. Joh NH, et al. Among authors: grigoryan g. Science. 2014 Dec 19;346(6216):1520-4. doi: 10.1126/science.1261172. Science. 2014. PMID: 25525248 Free PMC article.
Design of Specific Peptide-Protein Recognition.
Zheng F, Grigoryan G. Zheng F, et al. Among authors: grigoryan g. Methods Mol Biol. 2016;1414:249-63. doi: 10.1007/978-1-4939-3569-7_15. Methods Mol Biol. 2016. PMID: 27094296
Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials.
Holland J, Pan Q, Grigoryan G. Holland J, et al. Among authors: grigoryan g. PLoS One. 2018 Jun 28;13(6):e0199585. doi: 10.1371/journal.pone.0199585. eCollection 2018. PLoS One. 2018. PMID: 29953468 Free PMC article.
Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport.
Joh NH, Grigoryan G, Wu Y, DeGrado WF. Joh NH, et al. Among authors: grigoryan g. Philos Trans R Soc Lond B Biol Sci. 2017 Aug 5;372(1726):20160214. doi: 10.1098/rstb.2016.0214. Philos Trans R Soc Lond B Biol Sci. 2017. PMID: 28630154 Free PMC article. Review.
Sequence statistics of tertiary structural motifs reflect protein stability.
Zheng F, Grigoryan G. Zheng F, et al. Among authors: grigoryan g. PLoS One. 2017 May 26;12(5):e0178272. doi: 10.1371/journal.pone.0178272. eCollection 2017. PLoS One. 2017. PMID: 28552940 Free PMC article.
Quantitative insights have been gained by defining geometric descriptors of structure (e.g., distances, dihedral angles, solvent exposure, etc.) and observing their distributions and sequence preferences. ...
Quantitative insights have been gained by defining geometric descriptors of structure (e.g., distances, dihedral angles, solvent expo …
Protein structural motifs in prediction and design.
Mackenzie CO, Grigoryan G. Mackenzie CO, et al. Among authors: grigoryan g. Curr Opin Struct Biol. 2017 Jun;44:161-167. doi: 10.1016/j.sbi.2017.03.012. Epub 2017 Apr 28. Curr Opin Struct Biol. 2017. PMID: 28460216 Free PMC article. Review.
Simplifying the Design of Protein-Peptide Interaction Specificity with Sequence-Based Representations of Atomistic Models.
Zheng F, Grigoryan G. Zheng F, et al. Among authors: grigoryan g. Methods Mol Biol. 2017;1561:189-200. doi: 10.1007/978-1-4939-6798-8_11. Methods Mol Biol. 2017. PMID: 28236239
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