This paper reviews graph-theory-based methods that were recently developed in our group
for post-processing molecular dynamics trajectories. We show that the use of algorithmic …

Background: Macromolecule structure prediction remains a fundamental challenge of
bioinformatics. Over the past several decades, the Rosetta framework has provided …

For more than three decades, RNA has been known to be a relevant and attractive
macromolecule to target but figuring out which RNA should be targeted and how remains …

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density
functionals and basis sets. Traditionally, a particular density functional is chosen on the …

RNA (ribonucleic acid) structure prediction finds many applications in health science and
drug discovery due to its importance in several life regulatory processes. But despite …

Motivation Predicting the 3D structure of RNA molecules is a key feature towards predicting
their functions. Methods which work at atomic or nucleotide level are not suitable for large …

This chapter reviews advancements in computer‐aided design software for nucleic acid
nanostructures with some typical examples. It mainly focuses on DNA nanostructures …

Exploiting multi-core architectures is a way to tackle the CPU time consumption when
solving SATisfiability (SAT) problems. Portfolio is one of the main techniques that …

This paper reviews graph theory-based methods that were recently developed in our group
for post-processing molecular dynamics trajectories. We show that the use of algorithmic …

ABSTRACT RNA is the only member of the central dogma of biology that is able to
simultaneously store genetic information, and independently carry out a broad range of …