With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there
is a need for the tools used in protein-based drug design, particularly DOCKing algorithms …

DR_bind is a web server that automatically predicts DNA-binding residues, given the
respective protein structure based on (i) electrostatics,(ii) evolution and (iii) geometry. In …

A new method is introduced to structurally align interfaces observed in protein–DNA
complexes. The method is based on a procedure that describes the interfacial geometry in …

Abstract DNAproDB (https://dnaprodb. usc. edu) is a web-based database and structural
analysis tool that offers a combination of data visualization, data processing and search …

There has been a profound interest in designing small molecules that interact in sequence-
selective fashion with DNA minor grooves. However, most in silico approaches have not …

Drug discovery aims to identify potential therapeutic compounds capable of modulating the
activity of specific biological targets. Molecular docking can efficiently support this process …

How transcription factors (TFs) recognize their DNA sequences is often investigated
complementarily by high-throughput protein binding assays and by structural biology …

Motivation: Thousands of proteins are known to bind to DNA; for most of them the
mechanism of action and the residues that bind to DNA, ie the binding sites, are yet …

Protein complexes are involved in many important processes in living cells. To understand
the mechanisms of these processes, it is necessary to solve the 3D structures of the protein …

To investigate the principles driving recognition between proteins and DNA, we analyzed
more than thousand crystal structures of protein/DNA complexes. We classified protein and …