FREAD protocols

View FREAD computational protocol

FREAD statistics

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chevron_left Antibody structure prediction Loop modeling chevron_right
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FREAD specifications

Information


Unique identifier OMICS_05688
Name FREAD
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yoonjoo Choi <>

Publication for FREAD

library_books

FREAD revisited: Accurate loop structure prediction using a database search algorithm.

2010 Proteins
PMID: 20034110

FREAD in pipelines

 (3)
2017
PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] become far worse for loops beyond that length. there is an appreciable difference in accuracies achieved modelling h3 loops compared to the other cdrs. for example, the knowledge-based method fread has been shown to produce sub-ångström predictions for the five canonical cdrs (0.81  å, 0.42  å, 0.96  å, 0.98 å and 0.88  å for l1–h2), while the average accuracy for h3 loops is 2.25  å . […]

2017
PMCID: 5739537
PMID: 29199956
DOI: 10.7554/eLife.29023.046

[…] identified epitopes were obtained from the iedb ()., for the multiple ab test set, 12 abs were modeled from sequences () as described above. pdb code 4e9o:x was used for the vaccinia d8 structure. fread identified 2azw:a 87–91 (snhrq) as the best match for the missing loop from 207 to 209 (snheg), and this structural fragment was grafted into the model as described above., ag variants […]

2014
PMCID: 4031050
PMID: 24854015
DOI: 10.1371/journal.pcbi.1003636

[…] medeller server did not include target loops and were directly used for analysis. the two medeller models (3eml from 3uon and 1u7g from 3b9w) that included target loops were run again on the online fread server (http://opig.stats.ox.ac.uk/webapps/fread/php/index.php) and the best loop fragment hits excluding those from the target were used for analysis., homology modeling with modeller was run […]


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FREAD in publications

 (18)
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] chromatograms (xics) over all charge states., the crystal structure of bg505 nfl.664 was used as a template for md simulations. the disordered linker region (g509…………..s511) was modeled using the fread modeling server. we built the oligomannose glycans and then attached them to all n-glycosylation sites observed in crystal structure using the glycam webserver (http://www.glycam.org). […]

PMCID: 5727015
PMID: 29276518
DOI: 10.3389/fimmu.2017.01753

[…] constrains the geometry of the binding site, allowing for the third step, which is modeling of non-h3 cdrs. at this stage, either the canonical classes are used () or template-based modeling such as fread () or abgen (). in the final step, cdr-h3 is modeled using either homology or ab initio techniques (). the resultant antibody model is refined for feasibility of dihedral angles […]

PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] when a similar loop structure has not been observed previously, knowledge-based methods either give poor predictions or fail to return a prediction at all. examples of this type of algorithm include fread , , superlooper , loopweaver  and looping ., ab initio methods do not rely on previously observed structures; instead, decoys are produced computationally. ab initio methods work by exploring […]

PMCID: 5739537
PMID: 29199956
DOI: 10.7554/eLife.29023.046

[…] the crystal structure of unbound b7h6 was previously determined (pdb code: 3pv7) at 2.0 å. there is a missing loop in the crystal structure (chain a 150–157; dqvgmken). the loop was modeled using fread (; ) and a loop from 1o57:a 253–260 (stinmkek) was found to be the best match. anchor residues of the grafted loop (including backbone atoms) were minimized using the tinker molecular dynamics […]

PMCID: 5314778
PMID: 27915232
DOI: 10.1093/nar/gkw1198

[…] including all replicates and sequence variants were natural log transformed and rows and columns were hierarchically clustered using the ward.d2 algorithm., bed files were imported into r using fread (data.table), converted to genomicranges objects and sequences were retrieved from mm9, mm10 or rn5 genome versions using bsgenome objects and the getseq function (biostrings). iupac strings […]


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FREAD institution(s)
Department of Statistics, Oxford University, Oxford, UK

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