User profiles for Andrew M Watkins
Andrew WatkinsPostdoctoral Researcher in Biochemistry, Stanford University Verified email at stanford.edu Cited by 3097 |
Geometric deep learning of RNA structure
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 …
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 …
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
AlphaFold2 revolutionized structural biology with the ability to predict protein structures with
exceptionally high accuracy. Its implementation, however, lacks the code and data required …
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
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 …
including COVID-19. However, their optimization is hindered by mRNA instability and …
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
The discovery and design of biologically important RNA molecules is outpacing three-dimensional
structural characterization. Here, we demonstrate that cryo-electron microscopy can …
structural characterization. Here, we demonstrate that cryo-electron microscopy can …
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
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 …
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 …
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 …
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 …
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 …
that influence adipocyte differentiation or function. The perfluoroalkyl acids (PFAAs), used as …