SCPE : Structurally Constrained Protein Evolution 
 
Copyright (C) Gustavo Parisi and Julian Echave. 2001-2006
Contact: Gustavo Parisi: [email protected]

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
 
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.



DESCRIPTION

SCPE simulates sequence divergence under the structural constraints present in protein folds.
The program introduces random mutations in a sequence of known crystallographic structure and select them 
against to much structural deviation. The main output of the program is a whole set of site-specific 
substitutions matrices with their equilibrium frequencies. These files could be used in maximum 
likelihood calculations in programs of molecular evolution that allows the inclusion of site-specific matrices.
An excellent choice is the program HYPHY (http://www.hyphy.org). In SCPE web page there are some examples of script
files using SCPE matrices and HYPHY to perform maximum likelihood calculations. 


INSTALLATION


For the installation of SCPE in Lynux based systems first untar the file SCPE.tgz using


tar -xvf SCPE.tar

This will generate a directory called SCPEv1. 
Type in the command line 

make

This will compile the source generating the executable scpe.exe


USAGE


The input for a SCPE simulation is a file containing the coordinates of a protein structure. All the information for running the program 
is contained in a file called inputfile.in (the name is irrelevant).

The program takes the input file from the command line:

./scpe.exe inputfile.in


Bellow we reproduce the contents of the inputfile.in file. Lines starting with an asterisk are comments.



***************************************************************************************************************

*PDB INFORMATION

PDB FILENAME= ./PDB/1lxa.ent
PROTEIN CHAIN= A 


MULTIMER PROTEIN MODE = 0
HOMOOLIGOMER = 0
ALIGNMENT FILE = ./Example/lpxa70.fasta
*leaving empy the ALIGNMENT FILE only the pdb sequence will be taken for the simulations


*RUN INFORMATION

BETA FROM LIST = 0
LIST NAME = betalist.dat
INITIAL BETA PARAMETER= 0.15
SCREENING BETA-STEP= 0.2
MAXIMUM BETA= 0.40 

MUTATION MATRIX= QijCodonesEmp


INITIAL NUMBER OF ACCEPTED SUSTITUTIONS PER SITE= 10.0
STEP OF ACCEPTED SUSTITUTIONS PER SITE= 1000.0
MAXIMUM NUMBER OF ACCEPTED SUSTITUTIONS PER SITE= 200.0
NUMBER OF INDEPENDENT RUNS= 6000

*OUTPUT INFORMATION

RESULTS FILENAME= lpxa

*Name to be printed in HYPHY input matrices

MODEL NAME = lpxa
PATH TO RESULTS = 


************************************************************************************************************

In order to run SCPE a crystallographic structure for the reference protein should be available. The name of this file should be entered in the 
field "PDB FILENAME" and the name of the corresponding chain should be entered in "PROTEIN CHAIN". In the case that there is only one chain 
without any name, leave this field empty.

In the case the protein you are interested in is oligomeric, the field "MULTIMERIC PROTEIN MODE" should be activated with a "1". This  
forces the SCPE to take into account the protein-protein interactions between the different chain in the oligomers.  If the oligomer is a 
homo-oligomer put "1" in the field "HOMOOLIGOMER". If the oligomer is a heterooligomer write "0" in this field.

SCPE could take into account an alignment of homologous proteins containing the reference sequence (the one with known crystallographic structure). 
This alignment is used to derive initial amino acid distributions for each position. The format of this alignment should be FASTA and it should be 
edited in the way that the reference sequence does not contain gaps. Of course, gaps are allowed in other sequences (see an example included in the Example 
directory contained in the SCPE distribution)

SCPE contains a parameter called beta that is a measure of the selective pressure for structural conservation. In general a value of 0.15 
(field "INITIAL BETA PARAMETER") should be fine. However user could be interested in finding the beta parameter that better fit the substitution 
pattern in the protein of interest. In this case, the SCPE could take a series of beta values from a list "LIST NAME" that should be activate with 
a "1" in the field "BETA FROM LIST". In the case "BETA FROM LIST" is "0", SCPE should take the "INITIAL BETA PARAMETER" value, and each run add a 
given step "SCREENING BETA-STEP" until a maximum beta value is reached "MAXIMUM BETA". 

The field "INITIAL NUMBER OF ACCEPTED SUSTITUTIONS PER SITE" is a measure of the divergence reached at the end of the simulation. As explained before 
for the beta parameter, SCPE can run several runs for different number of accepted substitutions per site could be using the fields 
"STEP OF ACCEPTED SUSTITUTIONS PER SITE" and "MAXIMUM NUMBER OF ACCEPTED SUSTITUTIONS PER SITE".

Also should be indicated the number of independent runs in order to reach convergence. This value is strongly correlated with the length of the proteins. 
A number of 6000 independent runs is fine for a protein of about 250 residues.

The SCPE also uses a mutational matrix. The default mutation matrix is the one obtained by Scheider and collaborators 
(Scheneider, A, Cannarozzi, G and Gonnet, G "Empirical codon substitution matrix BMC Bioinformatics, 2006). 

Finally, other fields contain information about the output name files "RESULTS FILENAME", model name "MODEL NAME" and path to result files "PATH TO RESULTS".


If you use SCPE, please cite

* Structural constraints and emergence of sequence patterns in protein evolution. Parisi, G. and Echave, J. 
Molecular Biology and Evolution.18 (5): 750-756, 2001

* Quaternary structure constraints on evolutionary sequence divergence. Fornasari, MS, Parisi, G and Echave, J.  
Molecular Biology and Evolution, 24(2):349-51. 2007