Protein-DNA interactions are fundamental in biology, evolution, disease, and biotechnology.
This dissertation describes the use of state-of-the-art molecular modeling algorithms and …

Understanding the structural determinants of protein-DNA interactions can provide insight
for advancements in gene regulation, DNA repair mechanisms, as well as the development …

In search of its specific targets, a DNA-binding protein associates with nonspecific DNA and
subsequently diffuses along the DNA. Structural characterization of the nonspecific DNA …

Protein–protein and protein–DNA/RNA interactions are involved in many cellular processes.
Therefore, determining their complex structures at the atomic level is valuable to gain …

Nucleic acid–ligand interactions play an important role in numerous cellular processes such
as gene function expression and regulation. Therefore, nucleic acids such as RNAs have …

Recent developments in algorithms to predict the docking of two proteins have considered
both the initial rigid-body global search and subsequent screening and refinement. The …

Background Protein-DNA docking is a very challenging problem in structural bioinformatics
and has important implications in a number of applications, such as structure-based …

DNA-binding proteins play important roles in various cellular processes, but the
mechanisms by which proteins recognize genomic target sites remain incompletely …

DNA interacts with small molecules, from water to endogenous reactive oxygen and nitrogen
species, environmental mutagens and carcinogens, and pharmaceutical anticancer …

Interfacial water molecules play an important role in many aspects of protein–DNA specificity
and recognition. Yet they have been mostly neglected in the computational modeling of …