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

Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …

Macromolecular modeling and design are increasingly useful in basic research,
biotechnology, and teaching. However, the absence of a user-friendly modeling framework …

Advances over the past few years have begun to enable prediction and design of
macromolecular structures at near-atomic accuracy. Progress has stemmed from the …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Proteins with sequence-specific DNA binding function are important for a wide range of
biological activities. De novo prediction of their DNA-binding specificities from sequence …

The reprogramming of DNA-binding specificity is an important challenge for computational
protein design that tests current understanding of protein–DNA recognition, and has …

When a protein's function cannot be experimentally determined, it can often be inferred from
sequence similarity. Should this process fail, analysis of the protein structure can provide …

Motivation: Regulation of gene expression by a transcription factor requires physical
interaction between the factor and the DNA, which can be described by a statistical …