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AESOP Clustering Framework (Aug. 16, 2013)
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This README file describes the contents and usage of the AESOP Clustering Framework. 

Contents of AESOP_clust
------------------------
+ README (This file)
+ aesop_description.pdf =  Theory and structure behind the AESOP framework
+ Directories
  ------------
  - Source = Source code for AESOP framework, plus additional utilities to aid calculations
  	* AESOP.r    = Source code containing AESOP framework functions
	* pdb_align_hom.r  = Utility script for superimposing protein structures containing different sequences 
	* pdb_align.r      = Utility script for superimposing protein structures containing the same sequence
	* chimera_images.r = Utility script for making isopotential contours
  
  - examples = AESOP examples
  	+ barnase_alascan = Clustering example for alanine-scan of a single chain, barnase
		* Results (Folder)  = Contains example output files for comparison 
		* bn_bs.pdb         = PDB structure for the barnase-bastar complex (1BRS)
		* barnase_alascan.r = AESOP script for performing electrostatic similarity clustering of barnase alanine-scan mutants

  	+ barnase_barstar_alascan = Example for alanine-scan of a complex with clustering and solvation free energies of association
		* Results (Folder)    = Contains example output files for comparison 
		* barnase_barstar.pdb = PDB structure for the barnase-bastar complex (1BRS)
		* bnbs_alascan.r      = AESOP script for performing electrostatic similarity clustering and calculating solvation free energies
                                        of association for barnase-barstar alanine-scan mutants

  	+ c3d_perturb_map = Example for perturbation map of complement C3d
		* Results (Folder) = Contains example output files for comparison 
		* c3d.pdb          = PDB structure for the complement C3d (1C3D)
		* c3d_esi_dist.r   = AESOP script for generating perturbation map of 

  	+ LTP_homology = Clustering example for homologous lipid transfer proteins (LTP)
		* Results (Folder) = Contains example output files for comparison 
		* LTP_pdb (Folder) = Contains 20 PDB structures for LTP and LTP-like proteins from Arabidopsis
		* LTP_esd_clust.r  = AESOP script for performing electrostatic similarity clustering of LTPs  
		* chimera_images.r = Utility script for making isopotential contours for each LTP protein
		* pdb_align_hom.r  = Utility script for superimposing protein structures containing different sequences 
  
  	+ sumo_charge_reverse = Example for charge-reversal scan of SUMO4 in complex with SENP2 (clustering and free energies)
		* Results (Folder) = Contains example output files for comparison 
		* senp2_sumo4.pdb  = PDB file for the SENP2-SUMO4 complex (model)
		* sumo_qrev.r      = AESOP script for performing electrostatic similarity clustering and calculating solvation 
				     free energies of association for SENP2-SUMO4 charge-reversal scan mutants

  	+ sumo_mut_comb = Example for generating combinations of mutations based on list allowed mutations for SENP2-SUMO4 (clustering and free energies)
		* Results (Folder) = Contains example output files for comparison 
		* senp2_sumo4.pdb  = PDB file for the SENP2-SUMO4 complex (model)
		* sumo_mut_comb.r  = AESOP script for performing electrostatic similarity clustering and calculating solvation 
				     free energies of association for mutation combinations

  	+ c3d_mutants_list / cr2_mutants_list = Example for generating generating a list of specific mutations for C3d-CR2 (clustering and free energies)
		* Results (Folder) = Contains example output files for comparison 
		* c3d_cr2.pdb  = PDB file for the C3d-CR2 complex (model)
		* c3dmuts.xls / cr2muts.xls      = Excel file for the C3d/CR2 sequence number and mutant (up to triple mutants)
		* c3d_mut_list.r / cr2_mut_list.r  = AESOP script for performing electrostatic similarity clustering and calculating solvation 
				     free energies of association for specified list of SUMO4 mutants


External Software Needed for AESOP:
-----------------------------------
The following list of software must be installed prior to using the AESOP Framework. SCWRL4 is need for 
non-alanine mutations. The last two programs are needed only for the chimera_images (UCSF Chimera) and 
pdb_align_hom (MUSCLE) utilities, which have been included to aid in the visualization of results and 
in the super-positioning of homologous protein structures. Please visit the links below and follow the 
instructions provided by each website on how to install the programs. Where the programs are installed 
is not of importance, however the path to MUSCLE executable must be added to the PATH environmental 
variable. The paths to all other programs will simply be set in the AESOP scripts. At this time the AESOP 
Framework has only been tested for UNIX platforms (Mac and Linux), since PDB2PQR is unable to installed
on Windows. Those wishing to implement the AESOP framework on a Windows machine will need to use the 
Cygwin environment (http://www.cygwin.com/).
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R for Statistical Computing - http://www.r-project.org/

Bio3D - http://mccammon.ucsd.edu/~bgrant/bio3d/

APBS - http://www.poissonboltzmann.org/apbs/

PDB2PQR - http://www.poissonboltzmann.org/pdb2pqr/

UCSF Chimera - http://www.cgl.ucsf.edu/chimera/ (Needed for chimera_images to make isopotential contours)

**MUSCLE - http://www.drive5.com/muscle/ (Needed for pdb_align_hom to select atoms to be used in fitting)

**  Only needed for optional utilities for structure alignment and visualization
========================================================
One additional R package is also needed. It can be installed
by executing the following command while in the R environment:

install.packages("stringr")


Setup and execution of AESOP:
-----------------------------------
After installing the above required software, the paths of these programs must be updated in the AESOP_paths.r
file, which can be found in the source directory. To run an AESOP script, open the R environment and navigate 
to the correct working directory. Finally, the source command is used to execute the the AESOP script. Please 
see the aesop_description.pdf, and the included examples for more details.


***NOTE*** 
To avoid potential problems, it is best to use cleaned PDB files as input, meaning only including ATOM lines.
PDB files do not need to be renumbered, but if multiple chain are present in the PDB file, chain identifiers 
need to be used.