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

Transcription factors are proteins that bind to short sequence motifs on DNA typically called
cis-regulatory elements. These cis-regulatory elements are characterized by their linear …

Computational docking is an instrumental method of the structural biology toolbox.
Specifically, integrative modeling software, such as LightDock, arise as complementary and …

Molecular modeling by means of docking and molecular dynamics (MD) has become an
integral part of early drug discovery projects, enabling the screening and enrichment of large …

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 …

We consider the identification of interacting protein-nucleic acid partners using the rigid
body docking method FTdock, which is systematic and exhaustive in the exploration of …

Molecular docking is a traditional in silico method to obtain the structure of multi-molecule
complexes, allowing to get a deeper insight into the functions of the biologically important …

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and
functional genome. Yet, our structural understanding of how proteins interact with DNA is …

ABSTRACT We explored the Protein Data-Bank (PDB) to collect protein-ssDNA structures
and create a multiconformational docking benchmark including both bound and unbound …

In this review, we retraced the '40-year evolution'of molecular docking algorithms. Over the
course of the years, their development allowed to progress from the so-called 'rigid …