FRAGFOLD protocols

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FRAGFOLD specifications

Information


Unique identifier OMICS_19202
Name FRAGFOLD
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 4.8
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Jones <>

Publications for FRAGFOLD

FRAGFOLD in pipelines

 (2)
2017
PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1

[…] and accumulated accordingly. for each structure in the predicted ensemble, tm-score was calculated against each of the nmr models included in the pdb file. for each structure in the final fragfold-idp ensemble, the highest tm-score was selected. as all of the structures in the predicted ensemble had their tm-scores calculated, the mean tm-score was then computed., this averaging […]

2014
PMCID: 3956894
PMID: 24637808
DOI: 10.1371/journal.pone.0092197

[…] methods enabled a significant boost in the quality of de novo structure predictions. here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm – fragfold, with psicov, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. using a comprehensive set of 150 […]


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FRAGFOLD in publications

 (12)
PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1

[…] used to study idps, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. here, we present a new de novo method, fragfold-idp, which addresses this problem. using 200 protein structural ensembles derived from nmr, we show that fragfold-idp achieves superior results compared to methods which can predict related […]

PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] using the in-house threading methods pgenthreader (lobley et al., 2009) and pdomthreader (lobley et al., 2009) guided by the protein secondary-structure prediction method psipred (jones, 1999). the fragfold algorithm is used, where appropriate, to create ab initio models. fragfold uses known protein super-secondary-structural fragments and uses a simulated-annealing algorithm to assemble […]

PMCID: 5113899
PMID: 27855178
DOI: 10.1371/journal.pone.0164047

[…] film3: the program film3 [] is a specialised version of the mempack program [, ] incorporating correlated mutation constraints. these programs follow the fragment assembly approach of the fragfold program but adapted for tm-proteins to include a pre-calculation of the tm-segments and an optional constraint that can be applied to their residue positions relative to the membrane […]

PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] contact predictions (sequence separation >23) for a protein of length l were shown to have a precision greater than 0.5. these contact predictions were then used in the fragment-assembly software fragfold (), generating accurate models for 100 of the 150 targets. psicov predictions were also used with film3 to assist in protein structure prediction for 28 membrane proteins, producing accurate […]

PMCID: 4694711
PMID: 26713437
DOI: 10.1371/journal.pcbi.1004661

[…] amino-acid sequence and folds the protein by applying standard distance geometry techniques and simulated annealing with bonded and non-bonded potentials []., the fragment-based folding algorithm fragfold [,] was used in combination with the contact prediction method psicov [] for ab initio structure prediction []. the restraints were scored with a square well function with exponential […]


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FRAGFOLD institution(s)
Bioinformatics Unit, Department of Computer Science, University College London, London, UK; Department of Biochemistry and Molecular Biology, University College London, London, UK
FRAGFOLD funding source(s)
Supported by Joint Research Councils, Biotechnology and Biological Sciences Research Council, Department of Trade and Industry, Wellcome Trust, European Union Framework BioSapiens Network of Excellence and Medical Research Council.

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