FFAS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FFAS
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Tool usage distribution map

This map represents all the scientific publications referring to FFAS per scientific context
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Associated diseases

This word cloud represents FFAS usage per disease context
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Protocols

FFAS specifications

Information


Unique identifier OMICS_15567
Name FFAS
Alternative names Fold and Function Assignment System, FFAS03
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_15567
Name FFAS
Alternative names Fold and Function Assignment System, FFAS03
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An amino acid sequence.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Documentation


Maintainer


This tool is not available anymore.

Publications for Fold and Function Assignment System

FFAS citations

 (150)
library_books

Clostridium sordellii outer spore proteins maintain spore structural integrity and promote bacterial clearance from the gastrointestinal tract

2018
PLoS Pathog
PMCID: 5927469
PMID: 29668758
DOI: 10.1371/journal.ppat.1007004

[…] ns observed predominantly in the N- and C-terminus of the protein. CsA contains 8.5% cysteine residues, also making it a cysteine rich protein. Analysis using the Fold and Function Assignment server (FFAS, http://ffas.sanfordburnham.org [] failed to identify any known protein folds, nor were any conserved domains identified. No transmembrane domains were identified using TMpred (https://embnet.vit […]

call_split

Structural and Regulatory Changes in PBP4 Trigger Decreased β Lactam Susceptibility in Enterococcus faecalis

2018
MBio
PMCID: 5885037
PMID: 29615500
DOI: 10.1128/mBio.00361-18
call_split See protocol

[…] rmed on a CFX96 Real-Time PCR System (Bio-Rad), and the temperature was increased from 4°C and to 80°C in 0.2°C increments. Data were analyzed with the Bio-Rad CFX manager 3.1 software and SigmaPlot. FFAS () was used to identify the structures most similar to the sequence of PBP4; 1MWR was selected within FFAS to generate a model of PBP4. […]

call_split

Molecular Mechanisms Underlying Curcumin Mediated Therapeutic Effects in Type 2 Diabetes and Cancer

2018
PMCID: 5884026
PMID: 29743988
DOI: 10.1155/2018/9698258
call_split See protocol

[…] the mitochondrial capacity for energy expenditure, where glucose or lipids is/are used for energy production.It has been becoming clear that hyperlipidemia, reflected by chronically increased plasma FFAs, leads to an increased uptake of FFAs by the muscle cell and the production of intramuscular fatty acid metabolites (i.e., long-chain acyl-CoA, diacylglycerol, TGs, and ceramides) which stimulate […]

call_split

How ligand binds to the type 1 insulin like growth factor receptor

2018
Nat Commun
PMCID: 5826941
PMID: 29483580
DOI: 10.1038/s41467-018-03219-7
call_split See protocol

[…] 3LOH); whereas a search object for Fv 24–60 was generated from the structure of an anti-BclA scFv (PDB entry 3UMT; unpublished), modified by replacing all non-identical residues with serine using the FFAS03 server,. The MR search employed the anisotropy-corrected diffraction data set, as attempts using the complete data set failed. The initial model was refined against all data to 3.0 Å resolution […]

library_books

A peculiar IclR family transcription factor regulates para hydroxybenzoate catabolism in Streptomyces coelicolor

2017
Nucleic Acids Res
PMCID: 5814911
PMID: 29240934
DOI: 10.1093/nar/gkx1234

[…] S. coelicolor PobR has N- and C-terminal domains that each exhibit homology with IclR family transcription factors (Figure ; the two domains of PobR were also predicted to be structurally similar by FFAS (,)). With respect to its domain organization, PobR is atypical among IclR family members and transcription factors in general. Protein BLAST analyses () against streptomycete genomes in the IMG […]

library_books

ATM and CDK2 control chromatin remodeler CSB to inhibit RIF1 in DSB repair pathway choice

2017
Nat Commun
PMCID: 5715124
PMID: 29203878
DOI: 10.1038/s41467-017-02114-x

[…] acR–RIF1-C (Fig.  and Supplementary Fig. ), suggesting that the last 65 amino acids of CSB is necessary for its interaction with RIF1. Profile–profile alignment and fold-recognition using the program FFAS revealed that the last 76 amino acids of CSB resembled a winged helix domain (WHD) (Supplementary Fig. ). Additional protein threading trials using PHYRE (http://www.sbg.bio.ic.ac.uk/) strengthen […]


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FFAS institution(s)
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA; Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
FFAS funding source(s)
Supported by National Institute of Health (GM087218 and GM101457).

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