The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …

Computer-aided drug discovery/design methods have played a major role in the
development of therapeutically important small molecules for over three decades. These …

As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber …

We use computational design coupled with experimental characterization to systematically
investigate the design principles for macrocycle membrane permeability and oral …

Genome sequencing projects have resulted in a rapid increase in the number of known
protein sequences. In contrast, only about one-hundredth of these sequences have been …

Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks
generally have shapes that have evolved to fit precisely into binding pockets on their targets …

The quality of model structures generated by contemporary protein structure prediction
methods strongly depends on the degree of similarity between the target and available …

We have recently completed a full rearchitecturing of the Rosetta molecular modeling
program, generalizing and expanding its existing functionality. The new architecture enables …

Three-dimensional protein structures provide invaluable information for understanding and
regulating biological functions of proteins. The GalaxyWEB server predicts protein structure …

CHARMM‐GUI, http://www. charmm-gui. org, is a web‐based graphical user interface that
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …