New restraints and validation approaches for nucleic acid structures in PDB-REDO.

ABSTRACT: The quality of macromolecular structure models crucially depends on refinement and validation targets, which optimally describe the expected chemistry. Commonly used software for these two procedures has been designed and developed in a protein-centric manner, resulting in relatively few established features for the refinement and validation of nucleic acid-containing structure models. Here, new nucleic acid-specific approaches implemented in PDB-REDO are described, including a new restraint model using noncovalent geometries (base-pair hydrogen bonding and base-pair stacking) as refinement targets. New validation routines are also presented, including a metric for Watson-Crick base-pair geometry normality (Z_bpG). Applying the PDB-REDO pipeline with the new restraint model to th

SUBMITTER: de Vries I 

PROVIDER: S-EPMC8411979 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature