Determination of Allowable Conformations for 16S rRNA Based on Chemical Footpriting Data

This project, supported by NIH NLM-05652 and the Culpeper Foundation, is part of the Helix Group at the Stanford Section on Medical Informatics. Please address inquiries to altman@smi.stanford.edu.

Computational Methods for Determining the Allowable Conformational Space of 16S rRNA Based on Chemical Footprinting Data

Fink, D., Chen, R., Noller, H., and Altman, R.

Model information and coordinates

1. Mean position and variance of 65 helix centers of mass. This file summarizes the position of the centers of mass for each of the 65 helices positioned in our model. The file contains the helix ID (based on Figure 1 of paper), the mean x y and z position, as well as the variance in x y and z directions and the covariances for xy xz and yz.
2. Mean position and variance of modeled phosphates This file summarizes the MEAN position for the phosphates contained within the modeled helices. It is in PDB format. The mean position is given as the x,y,z coordinates, and the B-factor field is used to report the volume of variation for each phosphate. Because these are average positions, they may not satisfy detailed assessments of packing and stereochemistry.
3. Three approximate structures selected from the distribution of possible structures. The stereochemistry within helices is roughly correct, and packing violations are minimized, within the precision (15 - 25 Angstroms) allowed by the model. The three instances correspond to the First, second, and third instances shown in Figure 5 of the paper.
4. Mean position and variance of protein positions. This summarizes the positions and variances of protein centers of mass for model. The position of S19 was modified in response to inconsistencies in the data. S20 was not used in our model building effort due to possible problems with its neutron-diffraction defined position.
5. VRML representation of a sample model. This is an input file for the Virtual Reality Modeling Language (VRML) that is available on many web browsers, to look at a single 3D model that we have constructed. THIS IS COMING SOON.