User profiles for Andrew M Watkins

Andrew Watkins

Postdoctoral Researcher in Biochemistry, Stanford University
Verified email at stanford.edu
Cited by 3097

Geometric deep learning of RNA structure

…, S Eismann, AM Watkins, R Rangan, M Karelina… - Science, 2021 - science.org
RNA molecules adopt three-dimensional structures that are critical to their function and of
interest in drug discovery. Few RNA structures are known, however, and predicting them …

Variations in promoter activity reveal a differential expression and physiology of glutamate transporters by glia in the developing and mature CNS

…, MI Dykes-Hoberg, L Jin, AM Watkins… - Journal of …, 2007 - Soc Neuroscience
Glutamate transporters regulate excitatory neurotransmission and prevent glutamate-mediated
excitotoxicity in the CNS. To better study the cellular and temporal dynamics of the …

OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

…, A Ojewole, ME Guney, S Biderman, AM Watkins… - Biorxiv, 2022 - biorxiv.org
AlphaFold2 revolutionized structural biology with the ability to predict protein structures with
exceptionally high accuracy. Its implementation, however, lacks the code and data required …

[HTML][HTML] Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

…, K Fujii, E Sharma, AM Watkins… - Nature …, 2022 - nature.com
Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases,
including COVID-19. However, their optimization is hindered by mRNA instability and …

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang… - Nature …, 2020 - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-dimensional
structural characterization. Here, we demonstrate that cryo-electron microscopy can …

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

…, M Szachniuk, S Tian, J Wang, J Wang, AM Watkins… - Rna, 2020 - rnajournal.cshlp.org
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …

Theoretical basis for stabilizing messenger RNA through secondary structure design

…, JJ Nicol, R Wellington-Oguri, AM Watkins… - Nucleic acids …, 2021 - academic.oup.com
RNA hydrolysis presents problems in manufacturing, long-term storage, world-wide delivery
and in vivo stability of messenger RNA (mRNA)-based vaccines and therapeutics. A largely …

Anatomy of β-strands at protein–protein interfaces

AM Watkins, PS Arora - ACS chemical biology, 2014 - ACS Publications
The development of inhibitors for protein–protein interactions frequently involves the mimicry
of secondary structure motifs. While helical protein–protein interactions have been heavily …

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

R Rangan, AM Watkins, J Chacon… - Nucleic acids …, 2021 - academic.oup.com
The rapid spread of COVID-19 is motivating development of antivirals targeting conserved
SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA …

The effects of perfluorinated chemicals on adipocyte differentiation in vitro

AM Watkins, CR Wood, MT Lin, BD Abbott - Molecular and cellular …, 2015 - Elsevier
The 3T3-L1 preadipocyte culture system has been used to examine numerous compounds
that influence adipocyte differentiation or function. The perfluoroalkyl acids (PFAAs), used as …