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STACCATO
 
STACCATO

STACCATO will output a sequence alignment, given a collection of superimposed PDB files. You can then feed the output to secseq to illustrate the alignment, as for publication. The coordinates are input to STACCATO in separate PDB files. These are usually generated by MAPS.

STACCATO aims to solve the following problems: 
(1) Given multiple structures, superimposed by some multiple
structure alignment (MSA) method, optimize the muliple sequence
alignment consistent with the given structural alignment.

(2) Compute the sequence-structure conservation.

(3) Given a set of protein structures and a set of sequences,
compute a MSA of the two sets, which is consistent with a
structural alignment of the structure set.

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INPUT FILES
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  • Step 1: Make a file called "filelist" containing a list of all the PDB files that you wish to include in the alignment. For example, "filelist" would contain the following names: 
    csos3_18o_z.pdb
pdb1ddz_mono_cterm.pdb_maps
pdb1ddz_mono_nterm.pdb_maps
pdb1ekj_mono.pdb_maps
pdb1g5c_mono.pdb_maps
pdb1i6p_mono.pdb_maps
pdb1ylk_mono.pdb_maps
pdb1ym3_mono.pdb_maps

  • Step 2: make secondary structure assignments for all PDB files
    mkdssps -f filelist

  • Step 3: Run staccato
    staccato csos3_18o_z.pdb pdb1ddz_mono_cterm.pdb_maps pdb1ddz_mono_nterm.pdb_maps pdb1ekj_mono.pdb_maps pdb1g5c_mono.pdb_maps pdb1i6p_mono.pdb_maps pdb1ylk_mono.pdb_maps pdb1ym3_mono.pdb_maps

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    OUTPUT FILES
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    You'll get a log file (log_staccato.txt) that looks like this: 
    Alignment:
csos3_18o_   151> ---------------ADSASAIGFFLDCGFHAVDISPCADGRLKGLLPYI
pdb1ddz_mo   396> ------------------------------PEILWIGCADSRVP--ANQI
pdb1ddz_mo   142> ------------------------------PEYLWIGCADSRVP--ANQL
pdb1ekj_mo   153> ------------------------------PPFMVFACSDSRVC--PSHV
pdb1g5c_mo    25> ------------------------------PKLCIITCMDSRLIDLLERA
pdb1i6p_mo    35> ------------------------------PRFLWIGCSDSRVP--AERL
pdb1ylk_mo     1> ---GTVTDDYLANNVDYASGFKGPLPMPPSKHIAIVACMDARLD--VYRM
pdb1ym3_mo     4> TNPVAAWKALKEGNERFVAGRPQHPSQSQKPTAVIFGCADSRVA--AEII
                                                       * * *
                  33388888888888888888888888887734333220213124454443

csos3_18o_   186> LRLPLTAFTYRKAYAGSMFDI-----EDDLAQWEKNELRRYREGVPNTAD
pdb1ddz_mo   414> INLPAGEVFVHRNIANQCIHSD----MSFLSVLQYAVQYL----------
pdb1ddz_mo   160> LDLPAGEVFVHRNIANQCIHSD----ISFLSVLQYAVQYL----------
pdb1ekj_mo   171> LDFQPGEAFVVRNVANLVPPYDQAKYAGTGAAIEYAVLHL----------
pdb1g5c_mo    45> LGIGRGDAKVIKNAGNIVD-------DGVIRSAAVAIYAL----------
pdb1i6p_mo    53> TGLEPGELFVHRNVANLVIHTD----LNCLSVVQYAVDVL----------
pdb1ylk_mo    46> LGIKEGEAHVIRNAGCVVT-------DDVIRSLAISQRLL----------
pdb1ym3_mo    62> FDQGLGDMFVVRTAGHVID-------SAVLGSIEYAVTVL----------

                  33344234324223234355653333444334433334433333333333



    
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    STACCATO runs on Linux machines. The executable is:

    
/joule2/programs/lx_bin/staccato  or just type "staccato"

    

    The program is installed in /joule2/programs/staccato/staccato-linux-1.3.1:

    The program is available from http://bioinfo3d.cs.tau.ac.il/staccato/

    The documentation is available from /joule2/programs/staccato/README

    The contents of the README file are pasted below:
    *************************************************************
    README
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    1. Prepare aligned pdb files. You can use any method for multiple protein
structural alignment, as long as it can create transformed pdb files.  In case
you use MultiProt, http://bioinfo3d.cs.tau.ac.il/MultiProt/, then apply the
following script (script is located in the MultiProt installation directory):

>trans_mult.pl 17_sol.res 0 Trans

where:

17_sol.res: file produced by MultiProt which stores multiple alignments for 17 structures.
0:          solution number from 17_sol.res
Trans:    name of a directory where you want to copy transformed pdb files


2. Go to 'Trans' (or what ever the name is) directory.

It is very recommended to use Secondary Structure Information during MSA which
is structure based. This helps to use different scoring for regions that are either SSE's or loops.

Prepare DSSP (http://www.cmbi.kun.nl/gv/dssp/) files. This script creates dssp file for each pdb file.

>mkdssps 


Now you are ready to run the program:

>staccato 


3. Aligning structures and sequences:

>staccato pdb1 pdb2 ... -fasta seq1 seq2 ...

each seqX file may include multiple sequences.
Sequences must come in FASTA format.

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    Reference:
    Nucleic Acids Research. (2004). 32, W503-W507. BioInfo3D: a suite of tools for structural bioinformatics. Maxim Shatsky, Oranit Dror, Dina Schneidman-Duhovny, Ruth Nussinov and Haim J. Wolfson