DOI: 10.5281/zenodo.21690
title: Protein Secondary-Structure Description With A Coarse-Grained Model: Code And Datasets In Activepapers Format

description: This file contains the supplementary material for the publication

<em>Protein secondary-structure description with a coarse-grained model</em><br>
by Gerald R. Kneller and K. Hinsen<br>
http://dx.doi.org/10.1107/S1399004715007191<br>
Acta Cryst. (2015). D<strong>71</strong>, 1411-1422

<strong>Datasets in this file</strong>

1) ScrewFit and ScrewFrame parameters for ideal secondary-structure elements

   Scripts:<br>
     /code/import_ideal_structures<br>
     /code/analyze_ideal_structures

1.1) The PDB files generated with Chimera

   /data/ideal_structures/3-10.pdb<br>
   /data/ideal_structures/alpha.pdb<br>
   /data/ideal_structures/beta-antiparallel.pdb<br>
   /data/ideal_structures/beta-parallel.pdb<br>
   /data/ideal_structures/pi.pdb

1.2) The corresponding MOSAIC datasets

   /data/ideal_structures/3-10<br>
   /data/ideal_structures/alpha<br>
   /data/ideal_structures/beta-antiparallel<br>
   /data/ideal_structures/beta-parallel<br>
   /data/ideal_structures/pi

1.3) The ScrewFit parameters

   /data/ideal_structures/screwfit/3-10<br>
   /data/ideal_structures/screwfit/alpha<br>
   /data/ideal_structures/screwfit/beta-antiparallel<br>
   /data/ideal_structures/screwfit/beta-parallel<br>
   /data/ideal_structures/screwfit/pi

1.4) The ScrewFrame parameters

   /data/ideal_structures/screwframe/3-10<br>
   /data/ideal_structures/screwframe/alpha<br>
   /data/ideal_structures/screwframe/beta-antiparallel<br>
   /data/ideal_structures/screwframe/beta-parallel<br>
   /data/ideal_structures/screwframe/pi

<br>
2) Statistics for ScrewFit and ScrewFrame parameters computed<br>
   for the ASTRAL SCOPe subset with less than 40% sequence identity.

   Scripts:<br>
     /code/astral_analysis<br>
     /code/fit_rho_distributions<br>
     /code/plot_histograms

2.1) The ASTRAL database (link to published ActivePaper)

   /data/astral_2.04

2.2) The histograms for the ScrewFit and ScrewFrame parameters<br>
     for the all-alpha and all-beta subsets

   /data/histograms/astral_alpha/screwfit<br>
   /data/histograms/astral_alpha/screwframe

   /data/histograms/astral_beta/screwfit<br>
   /data/histograms/astral_beta/screwframe

2.3) The Gaussians fitted to the peaks in the distributions for rho

   /data/fitted_rho_distributions/screwfit<br>
   /data/fitted_rho_distributions/screwframe

2.4) Plots

   /documentation/delta.pdf<br>
   /documentation/delta_q.pdf<br>
   /documentation/delta_r.pdf<br>
   /documentation/p.pdf<br>
   /documentation/rho-detail.pdf<br>
   /documentation/rho.pdf<br>
   /documentation/sigma.pdf<br>
   /documentation/tau.pdf

<br>
3) Comparison of secondary-structure identification between ScrewFrame<br>
   and DSSP.

   Script:<br>
     /code/compare_secondary_structure_assignments<br>
     /code/plot_histograms

3.1) The histograms of the lengths of secondary-structure elements

   /data/histograms/secondary_structure/length-alpha-dssp<br>
   /data/histograms/secondary_structure/length-alpha-screwframe<br>
   /data/histograms/secondary_structure/length-beta-dssp<br>
   /data/histograms/secondary_structure/length-beta-screwframe

3.2) The 2D histograms of the number of residues inside identified<br>
     secondary-structure elements

   /data/histograms/secondary_structure/n-alpha<br>
   /data/histograms/secondary_structure/n-beta

3.3) The distribution of rho inside alpha helices

   /data/histograms/secondary_structure/rho-alpha-dssp

3.3) Plots

   /documentation/lengths-alpha.pdf<br>
   /documentation/lengths-beta.pdf<br>
   /documentation/n-alpha.pdf<br>
   /documentation/n-beta.pdf<br>
   /documentation/rho-alpha-dssp.pdf

<br>
4) Illustration for myoglobin and VADC-1

   Scripts:<br>
     /code/import_myoglobin_vdac<br>
     /code/analyze_myoglobin<br>
     /code/analyze_vdac<br>
     /code/perturbation_analysis

4.1) Imported structures in MOSAIC format:<br>
     PDB code 1A6G for myoglobin<br>
     PDB code 2K4T for VDAC-1

   /data/myoglobin<br>
   /data/VDAC-1

4.2) Plots showing rho and delta

   /documentation/rho-myoglobin.pdf<br>
   /documentation/delta-myoglobin.pdf

4.3) Tube models for visualization with Chimera

   /documentation/myoglobin-tube.bld<br>
   /documentation/VDAC-1-tube.bld

4.4) Sensitivity to perturbations in the coordinates

   /documentation/rho-perturbed-myoglobin.pdf<br>
   /documentation/delta-perturbed-VDAC-1.pdf<br>
   /documentation/rho-perturbed-myoglobin.pdf<br>
   /documentation/delta-perturbed-VDAC-1.pdf<br>
   /documentation/myoglobin-perturbation.pdf<br>
   /documentation/VDAC-1-perturbation.pdf

5) Analysis of CA-only structures in the PDB

   Scripts:<br>
     /code/ca_analysis<br>
     /code/import_calpha_structures<br>
     /code/plot_histograms

5.1) Imported CA-only structures in MOSAIC format

   /data/pdb_ca_only_structures

5.2) Histograms for ScrewFrame parameters

   /data/histograms/ca_only_structures

5.3) Plots

   /documentation/delta_ca.pdf<br>
   /documentation/delta_q_ca.pdf<br>
   /documentation/delta_r_ca.pdf<br>
   /documentation/p_ca.pdf<br>
   /documentation/rho_ca.pdf<br>
   /documentation/sigma_ca.pdf<br>
   /documentation/tau_ca.pdf