PDB coordinates to Restraints
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PDB to 3D Restraints

This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.

Reference for stacking restraints:

Laurberg M, Asahara H, Korostelev A, Zhu J , Trakhanov S and Noller HF
Structural basis for translation termination on the 70S ribosome
Nature , 2008 Aug 14;454(7206):852-7.

Stereochemical restraints are important in crystallographic refinement, especially at low resolution and at initial stages of refinement and model building. Provided a PDB-file, which may be your very preliminary model build, lists of the most probable base stacking and base pairing interactions within RNA (or DNA) chains are generated. The stacking restraints can be used as custom restraints in CNS using the STACK add-on (described below) and pairing restraints as custom hydrogen bonding distance restraints in PHENIX. Stacking and basepairing interactions can be visualized in Pymol and settings for finding them manually adjusted in a subsequent run to meet the quality of your current build.

RNA/DNA base stacking restraints in crystallographic refinement

We developed a novel energy term E-stack, and its derivatives as an add-on module to CNS in facilitating custom RNA base stacking restraints in crystallographic refinement, based on the stacking criteria described by Yang et al. (2003):

... The criteria for stacking are the following: the distance between the two centers of the ring is < 5.7 Å , the vertical distance between the two base planes is < 2.7 Å , and the base angles are < 40 ° ...

In our implementation, normal vectors for each base plane are calculated as the eigenvector of the atomic-coordinate covariance tensor corresponding to the lowest eigenvalue. E-stack and its derivatives are calculated from the sum of an angular potential between normal vectors and two square-well distance potentials between geometrical centers and between geometric centers and stacking planes. Weighting terms for partial potentials were optimized according to Rfree.

Download the E-stack add-on module for CNS here.

Links of interest: