The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating
topological entities can be either useful or cumbersome. In recent decades, the importance …

The last decade has shown that there are an increasing numbers of known proteins that
contain linear open knots or slipknots in their native folded structure. In general, knots in …

Recent experiments have conclusively shown that proteins are able to fold from an
unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones …

Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In
Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging …

How knotted proteins fold has remained controversial since the identification of deeply
knotted proteins nearly two decades ago. Both computational and experimental approaches …

Among all RNAs, tRNA exhibits the largest number and the widest variety of post-
transcriptional modifications. Modifications within the anticodon stem loop, mainly at the …

Abstract Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular
simulations because of the advantage of efficient partitioning of atom pairs between the …

Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of
the proteins. Oftentimes, these regions are introduced into the protein scaffold for function …

DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the
most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI …