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