De novo design of b-helical polypeptides

Gideon Kowadlo, Nathan E. Hall and Antony W. Burgess

Ludwig Institute for Cancer Research

Archive Site

Supplementary Figure

Temperature annealing molecular dynamics parameter testing using Rhom18h. Five runs of a set of eight parameter combinations (starting temperature and time between 25K temperature decreases) were conducted. The histogram shows the mean total energy for each set of parameters (light gray), with error bars showing the absolute maximum and minimum values of the ensemble. The average deviation from the mean for each category is also shown (dark gray), which gives a measure of spread.  Based on this data we chose annealing parameters at 1000K for 5 ps. Click here for the figure

BetaPrec Used for calculating precession of the modelled b-helices

You will need to download the matlab files (and unzip them to run).  Click here for instructions.

Hexilator Mathematica Scripts -Used to generate initial Ca coordinates for b-helices

Download scripts and instructions.

General scripts 1 & 2
Rhomb script
Trig scripts 1 & 2

PDB files: PDB files below are available for download

RhombNG	Initial Model	heated	cooled	4ns 300K MD
Rhomb14l_a	pdb file	pdb file	pdb file	pdb file
Rhomb14l_b	pdb file	pdb file	pdb file	pdb file
Rhomb18l_a	pdb file	pdb file	pdb file	pdb file
Rhomb18l_b	pdb file	pdb file	pdb file	pdb file
Rhomb22l_a	pdb file	pdb file	pdb file	pdb file
Rhomb26l_a	pdb file	pdb file	pdb file	pdb file
Rhomb18h_a	pdb file	pdb file	pdb file	pdb file
Rhomb18h_b	pdb file	pdb file	pdb file	pdb file
Rhomb18h_hole	pdb file	pdb file	pdb file	pdb file
Rhomb18h_noasn	pdb file	pdb file	pdb file	pdb file
Rhomb18h_nogly	pdb file	pdb file	pdb file	pdb file
Rhomb22h_a	pdb file	pdb file	pdb file	pdb file
Rhomb22h_b	pdb file	pdb file	pdb file	pdb file
Rhomb22h_c	pdb file	pdb file	pdb file	pdb file
TriG
Tri12_a	pdb file	pdb file
Tri18_a	pdb file	pdb file	pdb file	pdb file
Tri18_b	pdb file	pdb file	pdb file	pdb file
Tri18_c	pdb file	pdb file	pdb file	pdb file
Tri24_a	pdb file	pdb file	pdb file	pdb file