Jeremiah Nelson Sims

Computational design of potent, broadly neutralizing anti-Nipah virus and Hendra virus miniproteins

This paper computationally designs thermostable miniproteins that neutralize Nipah and Hendra viruses with subnanomolar affinity and potent in vitro antiviral activity.

Improved protein binder design using -pairing targeted RFdiffusion

Conditioning RFdiffusion on edge beta-strand pairing yields specific binders to polar targets, with in silico success above 9.2% versus 0.98% for hotspot-only conditioning.

Designed miniproteins potently inhibit and protect against MERS-CoV

This study designs miniproteins that inhibit MERS-CoV by targeting the spike protein, showing broad neutralization and protective efficacy in mice.

Capsule-Based Single-Cell Genome Sequencing

This paper introduces a semi-permeable capsule for single-cell genome sequencing, enabling uniform coverage and minimal cross-contamination for detecting genomic variants.

Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding

The paper develops a method to assess solution properties of designed proteins using mass spectrometry and peptide barcoding, enabling analysis of large protein libraries.