Andrew Watkins
Andrew Watkins
Postdoctoral Researcher in Biochemistry, Stanford University
Verified email at
Cited by
Cited by
Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
Accurate de novo design of hyperstable constrained peptides
G Bhardwaj, VK Mulligan, CD Bahl, JM Gilmore, PJ Harvey, O Cheneval, ...
Nature 538 (7625), 329-335, 2016
Geometric deep learning of RNA structure
RJL Townshend, S Eismann, AM Watkins, R Rangan, M Karelina, R Das, ...
Science 373 (6558), 1047-1051, 2021
FARFAR2: improved de novo rosetta prediction of complex global RNA folds
AM Watkins, R Rangan, R Das
Structure 28 (8), 963-976. e6, 2020
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang, S Li, G Pintilie, ...
Nature methods 17 (7), 699-707, 2020
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
K Leppek, GW Byeon, W Kladwang, HK Wayment-Steele, CH Kerr, AF Xu, ...
Nature communications 13 (1), 1536, 2022
Anatomy of β-strands at protein–protein interfaces
AM Watkins, PS Arora
ACS chemical biology 9 (8), 1747-1754, 2014
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
Z Miao, RW Adamiak, M Antczak, MJ Boniecki, J Bujnicki, SJ Chen, ...
Rna 26 (8), 982-995, 2020
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
G Ahdritz, N Bouatta, C Floristean, S Kadyan, Q Xia, W Gerecke, ...
Nature Methods, 1-11, 2024
Theoretical basis for stabilizing messenger RNA through secondary structure design
HK Wayment-Steele, DS Kim, CA Choe, JJ Nicol, R Wellington-Oguri, ...
Nucleic acids research 49 (18), 10604-10617, 2021
Protein domain mimics as modulators of protein–protein interactions
N Sawyer, AM Watkins, PS Arora
Accounts of chemical research 50 (6), 1313-1322, 2017
Expanding the limits of the second genetic code with ribozymes
J Lee, KE Schwieter, AM Watkins, DS Kim, H Yu, KJ Schwarz, J Lim, ...
Nature communications 10 (1), 5097, 2019
Protein–protein interactions mediated by helical tertiary structure motifs
AM Watkins, MG Wuo, PS Arora
Journal of the American Chemical Society 137 (36), 11622-11630, 2015
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design
K Drew, PD Renfrew, TW Craven, GL Butterfoss, FC Chou, S Lyskov, ...
PLoS One 8 (7), e67051, 2013
Structure-based inhibition of protein–protein interactions
AM Watkins, PS Arora
European journal of medicinal chemistry 94, 480-488, 2015
De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures
R Rangan, AM Watkins, J Chacon, R Kretsch, W Kladwang, IN Zheludev, ...
Nucleic acids research 49 (6), 3092-3108, 2021
Designing peptides on a quantum computer
VK Mulligan, H Melo, HI Merritt, S Slocum, BD Weitzner, AM Watkins, ...
BioRxiv, 752485, 2019
Blind prediction of noncanonical RNA structure at atomic accuracy
AM Watkins, C Geniesse, W Kladwang, P Zakrevsky, L Jaeger, R Das
Science Advances 4 (5), eaar5316, 2018
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1
VK Mulligan, S Workman, T Sun, S Rettie, X Li, LJ Worrall, TW Craven, ...
Proceedings of the National Academy of Sciences 118 (12), e2012800118, 2021
HippDB: a database of readily targeted helical protein–protein interactions
CM Bergey, AM Watkins, PS Arora
Bioinformatics 29 (21), 2806-2807, 2013
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