Vectorbased protein representation code for stochastic roadmap simulation

M. Serkan Apaydin

12/09/2003

Warning: Absolutely no warranty.

This is the second part of the SRS code. The input data files for two proteins 
(pdb ID : 1ROP, a 2 helical protein, and 1HDD, a 3 alpha-helical protein) are
 also provided. 

Installation instructions:
----------------------------
tar xvfz srs_vectorBased.tgz
cd vectorBased
make

compiling/building meschach:  (if included meschach library does not work)
----------------------------

If the included meschach library (meschach/libmeschach.a) does not fit your
 system, you will have to rebuild it. To do this, go to meschach directory,
 and type:
make realclean
./configure --with-sparse
make sparse
make clean



Running instructions:
----------------------------
run ./predict_rmsd for running instructions.

a sample run could be:

./predict_rmsd 1ROP myRoadmap.txt Y Y 0 0 3 10 1000 

or

./predict_rmsd 1HDD myRoadmap.txt Y Y 0 0 5 10 1000 

the above (first) command creates a roadmap of 1000 nodes, and computes pfold for the
 first 81 nodes read from tests/1ROP/myRoadmap10002.txt. These pfold values 
are written to pfold1081_0.txt. 3 and 10 are the macrostate radii, in terms 
of RMSD. 
The provided 1ROPCyclicPfoldSummary.txt file contains pfold results obtained
 for those same 81 configurations using Monte Carlo simulation, again using
 3A and 10A as the radii of the macrostates.

For 1HDD, the corresponding macrostate radii are 5 and 10A.


in mFiles directory, run sampleMFile.m (in matlab) to plot a comparison of the
pfold results with SRS and Monte Carlo. The Monte Carlo pfold results are 
provided in 1ROPCyclicPfoldSummary.txt.