The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through
genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring …

We describe methods for physics-based protein design and some recent applications from
our work. We present the physical interpretation of a MC simulation in sequence space and …

Gene pairs that overlap in their coding regions are rare except in viruses. They may occur
transiently in gene creation and are of biotechnological interest. We have examined the …

Enzyme design is an important application of computational protein design (CPD). It can
benefit enormously from the additional chemistries provided by noncanonical amino acids (…

Designed enzymes are of fundamental and technological interest. Experimental directed
evolution still has significant limitations, and computational approaches are a complementary …

We propose a novel heuristic to predict RNA secondary structure formation pathways that
has two components: (i) a folding algorithm and (ii) a kinetic ansatz. This heuristic is inspired …

Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein
engineering, enabling new structural motifs and building blocks. To incorporate them into an …

Computational protein design (CPD) can address the inverse folding problem, exploring a
large space of sequences and selecting ones predicted to fold. CPD was used previously to …

We present a new educational initiative called Meet-U that aims to train students for collaborative
work in computational biology and to bridge the gap between education and research. …

This chapter describes two computational methods for PDZ–peptide binding: high-throughput
computational protein design (CPD) and a medium-throughput approach combining …