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chevron_left Loop modeling Antibody structure prediction chevron_right
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Protocols

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 citations

 (18)
library_books

Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

2018
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). […]

library_books

How B Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

2017
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 […]

library_books

Antibody H3 Structure Prediction

2017
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 […]

library_books

Computationally driven identification of antibody epitopes

2017
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 […]

library_books

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop seq

2016
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 […]

library_books

Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective

2016
PMCID: 4958977
PMID: 27453290
DOI: 10.1038/srep30105

[…] structure (pdb id: 1kv3; h. sapiens species; 2.1 å resolution) using the yasara structure package version 13.11.1. gaps or unresolved regions within the crystal structure(s) were modeled them on the fread loop modeling server (http://opig.stats.ox.ac.uk/webapps/fread/php/; accessed on 05.10.2014). for e.g. the pdb file 1f13 that is unresolved at the thrombin cleavage site arg37-gly38 […]


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

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