A5074471776- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Materials Science
- Retinal Development and Disorders
- Receptor Mechanisms and Signaling
- Viral Infections and Outbreaks Research
- Photoreceptor and optogenetics research
- Mosquito-borne diseases and control
- Calcium signaling and nucleotide metabolism
- Virus-based gene therapy research
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Historical and Contemporary Political Dynamics
- Metabolomics and Mass Spectrometry Studies
- Viral Infections and Vectors
- Complement system in diseases
- Adenosine and Purinergic Signaling
- Molecular Biology Techniques and Applications
- Viral gastroenteritis research and epidemiology
- vaccines and immunoinformatics approaches
- Virology and Viral Diseases
Tri-Institutional PhD Program in Chemical Biology
2020-2025
Cornell University
2020-2025
University of Nottingham
2025
Memorial Sloan Kettering Cancer Center
2020-2024
Kettering University
2024
University of California, Irvine
2023
University of Colorado Boulder
2023
University of Montana
2023
University of California, San Diego
2023
Open Geospatial Consortium
2023
A generalized and extensible machine-learned molecular mechanics force field trained on over 1.1 million QC data applicable for drug discovery applications. Figure reproduced from the arXiv:201001196 preprint under arXiv non-exclusive license.
A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, including standard and "barcode-aware" sampling. We demonstrate effective coverage enrichment assessment multiple human genomes copy number structural variation on a single flow cell.
A stabilized dimer of the surface protein from dengue virus has been engineered to elicit antibodies that neutralize virus.
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface systems is indispensable for biomolecular simulation computer-aided drug design. Here, we introduce a generalized machine-learned MM field, \texttt{espaloma-0.3}, an end-to-end differentiable framework using graph neural networks to overcome limitations traditional rule-based methods. Trained in single GPU-day fit large diverse quantum...
Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, blinding disease. Rhodopsin self-associates membrane, and purified monomeric apo-protein opsin dimerizes vitro as it transitions from detergent micelles to reconstitute into lipid bilayer. We previously reported that pigmentosa-linked F220C mutant fails dimerize vitro, reconstituting monomer. Using fluorescence-based assays molecular dynamics simulations we now report...
Abstract During the COVID-19 pandemic, structural biologists rushed to solve structures of 28 proteins encoded by SARS-CoV-2 genome in order understand viral life cycle and enable structure-based drug design. In addition 204 previously solved from SARS-CoV-1, 548 covering 16 have been released a span only 6 months. These models serve as basis for research how virus hijacks human cells, design, aid development vaccines. However, errors often occur even most careful structure determination -...
Abstract Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, blinding disease. Rhodopsin self-associates membrane, and purified monomeric apo-protein opsin dimerizes vitro as it transitions from detergent micelles to reconstitute into lipid bilayer. We previously reported that pigmentosa-linked F220C mutant fails dimerize , reconstituting monomer. Using fluorescence-based assays molecular dynamics simulations we now...