FATCAT is the software package behind https://fatcat.godziklab.org
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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, https://doi.org/10.1093/nar/gkaa443
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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
Run
./Install
If Install fails, please go to the FATCATMain directory and modify the basic.h file that includes all the head files. Then run
make
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purpose: run Flexible alignments for a pair of proteins with given options
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command: FATCAT [parameters...]
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for help: simply run FATCAT
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inputs: two protein structures, and an output name (eg. pdb1.pdb2)
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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 -- pdb1.pdb2.afp.ps (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
purpose: a script for runing FATCAT on a list of structure pairs
command: FATCATQue.pl log-file pair-list-file <parameters..>
purpose: a script for runing FATCAT for a query against a database command: FATCATQue.pl query target-list parameters.. note: for this purpose, you need to prepare a database of protein 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
inputs:
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
1a21A_1hwgC.afp.color.ps # 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.
Go to ./Examples2_FATCAT
command:
../FATCATMain/FATCATQue.pl 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:
command:
../FATCATMain/FATCATQue.pl timeused prtpair.list -q >prtpair.aln
(note: this calculation takes about 10 min on Intel(R) XEON(TM) CPU 1.80GHz)