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FATCAT specifications


Unique identifier OMICS_03639
Alternative name Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists
Interface Web user interface
Restrictions to use None
Input data Protein primary and secondary structures
Input format PDB
Programming languages C++, Perl
Computer skills Basic
Stability Stable
Maintained Yes


Publications for Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists

FATCAT citations


Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines

PLoS One
PMCID: 5919458
PMID: 29698445
DOI: 10.1371/journal.pone.0196349

[…] Visualization and analysis of protein structures were performed using the PyMol package []. Structure comparisons were performed using the FATCAT algorithm [] included in the protein comparison tool of the Protein Data Bank (PDB) web server. DaliLite v3 was used to search for structural related proteins []. […]


Transposase DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance

PMCID: 5871717
PMID: 29551265
DOI: 10.1016/j.cell.2018.02.032

[…] scribed in (). First, Int82N tetramers were assembled by superposing individual protein domains onto λInt–COC’ post-cleavage synaptic complex structure (PDB: 1z19) by rigid structural alignment using FATCAT (). Flexible parts that could not be aligned, including the β-hairpin insertion, were isolated and modeled separately with Phyre2 (). As Tn1549 Int’s helix αM is substituted with a short beta s […]


Expression correlates between Annexin A1 and A2 autoantibodies in patients with Behçet’s disease

Biosci Rep
PMCID: 5773811
PMID: 28963375
DOI: 10.1042/BSR20170778

[…] mitant of each other. Then, 3D structural similarity analysis was performed using flexible structural alignment method (flexible structure alignment by chaining aligned fragment pairs allowing twist (FATCAT)) [,]. […]


Functional Connectivity Alterations between Networks and Associations with Infant Immune Health within Networks in HIV Infected Children on Early Treatment: A Study at 7 Years

Front Hum Neurosci
PMCID: 5768628
PMID: 29375341
DOI: 10.3389/fnhum.2017.00635

[…] mith et al., ). Each IC was visually inspected and quantitatively compared to the standard set of Functional Connectome Project (FCP) template RSN maps (Biswal et al., ) using the 3dMatch function in FATCAT (Taylor and Saad, ). ICs containing known networks were thresholded at Z > 3 and binarized RSN masks created. The remaining ICs (representing non-GM tissue, subject motion, etc.) were discarded […]


Acquisition of functions on the outer capsid surface during evolution of double stranded RNA fungal viruses

PLoS Pathog
PMCID: 5738138
PMID: 29220409
DOI: 10.1371/journal.ppat.1006755
call_split See protocol

[…] p://ekhidna.biocenter.helsinki.fi/dali_server/start) was used for structural alignment between RnQV1 CP P2 and P4 proteins and their overlap with PcV CP A and B domains as well as L-A Gag CP. We used FATCAT [] (http://fatcat.burnham.org), CATH [] (http://www.cathdb.info) and Dali servers to search for structures related to the P2 Asp227-Tyr350 domain. […]


Protein Structure Insights into the Bilayer Interactions of the Saposin Like Domain of Solanum tuberosum Aspartic Protease

Sci Rep
PMCID: 5717070
PMID: 29208977
DOI: 10.1038/s41598-017-16734-2

[…] t peptides and 2S albumins. Additionally, a protein domain structure alignment search of the RCSB PDB structure database for PSI (3RFI; using the Protein Structure Comparison Tool v.4.2.0 running the FATCAT algorithm) produced high-scoring matches to diverse surface-active/membrane-interacting proteins including endosomal/vacuolar factors (endosomal sorting complex required for transport-I and vac […]


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FATCAT institution(s)
The Burnham Institute, La Jolla, CA, USA
FATCAT funding source(s)
This research was supported by NIH grant GM63208.

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