MELD-DNA: A new tool for capturing protein-DNA binding

Abstract

Herein we present MELD-DNA, a novel computational approach to address the problem of protein-DNA structure prediction. This method addresses well-known issues hampering current computational approaches to bridge the gap between structural and sequence knowledge, such as large conformational changes in DNA and highly charged electrostatic interaction during binding. MELD-DNA is able to: i) sample multiple binding modes, ii) identify the preferred binding mode from the ensembles, and iii) provide qualitative binding preferences between DNA sequences. We expect the results presented herein will have impact in the field of biophysics (through new software development), structural biology (by complementing DNA structural databases) and supramolecular chemistry (by bringing new insights into protein-DNA interactions).