Stephen joins the Gaurav Bhardwaj Lab via the Molecular & Cellular Biology PhD Program.

Publications

Cyclic peptide structure prediction and design using AlphaFold. Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. bioRxiv. 2023 Feb 26:2023.02.25.529956. doi: 10.1101/2023.02.25.529956. Preprint. PMID: 36865323

Accurate de novo design of membrane-traversing macrocycles. Bhardwaj G, O’Connor J, Rettie S, Huang YH, Ramelot TA, Mulligan VK, Alpkilic GG, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D. Cell. 2022 Sep 15;185(19):3520-3532.e26. doi: 10.1016/j.cell.2022.07.019. Epub 2022 Aug 29.

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Hosseinzadeh P, Watson PR, Craven TW, Li X, Rettie S, Pardo-Avila F, Bera AK, Mulligan VK, Lu P, Ford AS, Weitzner BD, Stewart LJ, Moyer AP, Di Piazza M, Whalen JG, Greisen PJ, Christianson DW, Baker D. Nat Commun. 2021 Jun 7;12(1):3384. doi: 10.1038/s41467-021-23609-8.
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, Baker D. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2012800118. doi: 10.1073/pnas.2012800118.
Computational design of mixed chirality peptide macrocycles with internal symmetry. Mulligan VK, Kang CS, Sawaya MR, Rettie S, Li X, Antselovich I, Craven TW, Watkins AM, Labonte JW, DiMaio F, Yeates TO, Baker D. Protein Sci. 2020 Dec;29(12):2433-2445. doi: 10.1002/pro.3974.

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD. Protein Sci. 2018 Sep; 9(27)1611-1623

Comprehensive computational design of ordered peptide macrocycles.  Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D.  Science. 2017 Dec 15; 6369(358)1461-1466

Accurate de novo design of hyperstable constrained peptides.  Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D.  Nature. 2016 Oct 20; 7625(538)329-335