FoldX accurate structural protein-DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1).

ABSTRACT: The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein-DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural complexes and predicts the DNA-binding regions of resolved protein structures. PADA1 relies on a library of protein and double-stranded DNA fragment pairs obtained from a training set of 2103 DNA-protein complexes. It includes a fast statistical force field computed from atom-atom distances, to evaluate and filter the 3D docking models. Using published benchmark validation sets and 212 DNA-protein structures published after 2016 we predicted the DNA-binding regions with an RMSD of <1.8 Å per residue in >95% of the cases. We show that the quality of the docked templates is

SUBMITTER: Blanco JD 

PROVIDER: S-EPMC5934639 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature