Here we present pyDockDNA, which is based on the pyDock program, with a new module
for reading and parsing DNA molecules. The protocol is composed of two major steps …

Most life science processes involve, at the atomic scale, recognition between two molecules.
The prediction of such interactions at the molecular level, by so-called docking software, is a …

Here, we describe two freely available web servers for molecular docking. The PatchDock
method performs structure prediction of protein–protein and protein–small molecule …

Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of
biological processes. Determining the complex structures of these interactions is valuable, in …

This article describes a GPU-based high-performance computing method to tackle the
protein-DNA docking problem. GPU-specific algorithmic techniques are developed to …

Accurate prediction of protein–DNA complexes could provide an important stepping stone
towards a thorough comprehension of vital intracellular processes. Few attempts were made …

The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long
been challenges that prevented the development of efficient protein–DNA docking methods …

Background Macromolecular docking is a challenging field of bioinformatics. Developing
new algorithms is a slow process generally involving routine tasks that should be found in a …

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