Biological processes such as transcription, repair, and regulation require interactions
between DNA and proteins. To unravel their functions, it is imperative to determine the high …

Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …

This chapter contains sections titled: Introduction The need for protein–protein and protein–
DNA docking Overview of the computational approach Scope of this chapter Structural …

Protein-DNA interactions are the physical basis of gene expression and DNA modification.
Structural models that reveal these interactions are essential for their understanding. As only …

Protein-DNA interactions play a crucial role in gene expression and regulation. Identifying
the DNA binding surface of proteins has long been a challenge–in comparison to protein …

Proteins binding to specific locations in DNA control gene expression, replication of DNA,
DNA repair, and other vital cellular processes. A fuller understanding of these interactions …

An accurate, predictive understanding of protein–DNA binding specificity is crucial for the
successful design and engineering of novel protein–DNA binding complexes. In this review …

Sunday, February 20, 2022 131a large electrostatic component of the interaction. This leads
to well known sampling and scoring failures in docking methodologies, which has limited the …

Abstract Characterization and prediction of the DNA-biding regions in proteins are essential
for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) …

Motivation: Computational modeling of protein–DNA complexes remains a challenging
problem in structural bioinformatics. One of the key factors for a successful protein–DNA …