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FATCAT package

(Flexible structural AlignmenT by Chaining AFPs with Twist)


FATCAT is the software package behind

  • Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik, FATCAT 2.0: towards a better understanding of the structural diversity of proteins, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W60–W64,

  • Ye Y, Godzik A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 2004;32(Web Server issue):W582-W585. http://doi:10.1093/nar/gkh430




If Install fails, please go to the FATCATMain directory and modify the basic.h file that includes all the head files. Then run


FATCAT usages

Program 1: FATCAT (main program)

  • purpose: run Flexible alignments for a pair of proteins with given options

  • command: FATCAT [parameters...]

  • for help: simply run FATCAT

  • inputs: two protein structures, and an output name (eg. pdb1.pdb2)

  • avaiable outputs:

    the short report of the results                --  to stdout (for system analysis)
    the detailed report of the results             --  to stdout (for system analysis)
    the alignment between two structures in text   --  to file or stdout (for system analysis)
    the chaining result in text file               --  pdb1.pdb2.chain.txt (for case study)
    the .ps file of all AFPs and final AFP chain   -- (for case study)
    pdbfiles based on block superimpose            --  pdb1.pdb2.(block-index).pdb
                                                       pdb1.pdb2.(block-index).script (for rasmol) (for case study)
    pdbfiles based on optimized block superimpose  --  pdb1.pdb2.(block-index).pdb
                                                       pdb1.pdb2.(block-index).script (for rasmol) (for case study)
    twisted structure based on blocks              --  pdb1.pdb2.ini.twist.pdb
                                                       pdb1.pdb2.ini.twist.script (for case study)               
    twisted structure after align optimization     --  pdb1.pdb2.opt.twist.pdb
                                                       pdb1.pdb2.opt.twist.script (for case study)                

note: all the output pdb files include two chains with chain A for pdb 1 and chain B for pdb 2

Program 2:

purpose: a script for runing FATCAT on a list of structure pairs

command: log-file pair-list-file <parameters..>

Program 3:

purpose: a script for runing FATCAT for a query against a database command: query target-list parameters.. note: for this purpose, you need to prepare a database of protein structures


1. FATCAT for a single pair of structures

Go to ./Examples_FATCAT,

run FATCAT for structure 1a21A.pdb and 1hwgC.pdb

command: FATCAT -p1 1a21A.pdb -p2 1hwgC.pdb -o 1a21A_1hwgC -m -ac -t

  structure 1a21A.pdb and 1hwgC.pdb

outputs: (a twist is detected in comparing these two structures)

  1a21A_1hwgC.aln               # alignment result between the two structures      # the AFP chaining result of the FATCAT in postscript graph
  1a21A_1hwgC.opt.twist.pdb     # the pdb file in which 1a21A.pdb in chain A, twisted 1hwgC.pdb in chain B  
			                    # refer REMARK lines in the begining of .pdb file
  1a21A_1hwgC.opt.twist.script  # the rasmol script for viewing 1a21A_1hwgC.opt.twist.pdb 
			                    # blocks of 1hwgC.pdb are shown in different colors
			                    # command: rasmol -script 1a21A_1hwgC.opt.twist.script

Please compare 1a21A_1hwgC.aln with compare.aln file. If no difference is found between these two files, FATCAT runs ok.

2. FATCAT for a list of pairs

Go to ./Examples2_FATCAT

 ../FATCATMain/ timeused allpair.list -q >allpair.aln
(note: this calculation takes about 30 min on Intel(R) XEON(TM) CPU 1.80GHz)

input: allpair.list (the list of pairs) and the corresponding pdb files
output: allpair.aln (the text file of all the alignments)

Please compare allpair.aln with allpair.aln.comp. If no difference is found, FATCAT runs ok.

for testing a smaller set of pairs:

../FATCATMain/ timeused prtpair.list -q >prtpair.aln

(note: this calculation takes about 10 min on Intel(R) XEON(TM) CPU 1.80GHz)


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