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FunFOLD specifications

Information


Unique identifier OMICS_03793
Name FunFOLD
Interface Web user interface
Restrictions to use None
Input data A protein sequence in single letter amino acid code.
Output data A list of putative ligand-binding site residues plus a list of the ligands within the binding site cluster.
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Subtool


  • FunFOLDQA

Maintainers


  • person_outline Liam J. McGuffin <>
  • person_outline Daniel Roche <>

Additional information


https://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_help_2_0.html

Publications for FunFOLD

FunFOLD citations

 (7)
library_books

Normal Modes Expose Active Sites in Enzymes

2016
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] [–]. several webservers of ligand binding sites have also been constructed and may be used to infer unknown ligand binding sites based on homology and other attributes such as pocketome [], funfold [], scpdb [], ibis [], multibind [], fpop [], and findsite []. to date however, no comprehensive study comparing geometry based techniques has been performed., normal-mode analysis is one […]

library_books

In silico characterization and Molecular modeling of double strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

2015
PMCID: 4635681
PMID: 26541955
DOI: 10.1186/s12976-015-0013-2

[…] []. one conserved residue in eukaryotic mre11 proteins, glu286 (fig. ), forms h-bonds with his253 and stabilizes this histidine. the same active site binding substrates were found using the funfold server [] and the 3dligandsite server [].fig. 4, comparing structures of hmsmre11 (homo sapiens, pdb : 3t1i) [], pfmre11 (pyrococcus furiosus, archaea pdb id: 1ii7, []), sp mre11 […]

library_books

Molecular Dynamic Simulations Reveal the Structural Determinants of Fatty Acid Binding to Oxy Myoglobin

2015
PMCID: 4451517
PMID: 26030763
DOI: 10.1371/journal.pone.0128496

[…] in mb is unknown, we sought to computationally predict the ligand-binding site. there are several methods that may be employed, including q-site finder [], sitehound-web [], coach [], biolip [], and funfold2 []. despite their utility, these methods are challenging to apply to predictions in which the comparator proteins are structurally dissimilar and exhibit high sequence divergence. […]

library_books

Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain — Implication in Mechanosensing

2014
PMCID: 3983058
PMID: 24722239
DOI: 10.1371/journal.pcbi.1003532

[…] ii–iv) other than i27's. both f unfold (, top side panel) and δl (, right side panel) were broadly distributed, ranging from 30 to 120 pn and from 5 to 120 nm, respectively. the unfolding peak force funfold and contour length change δl showed no correlations since no dominant region can be found in . the relationship between funfold and δl as well as their distributions indicate that within […]

library_books

Structural and mechanical properties of individual human telomeric G quadruplexes in molecularly crowded solutions

2013
PMCID: 3616730
PMID: 23396442
DOI: 10.1093/nar/gkt038

[…] range (see supplementary data for detailed calculation)., force-based single-molecule approach has an additional and unique advantage to reveal mechanical properties, such as unfolding force, funfold, of a biomolecule. in diluted buffers, it has been discovered that funfold of g-quadruplexes () is significantly higher than the stall force of many motor proteins, such as dna and rna […]

library_books

Structure and evolution of barley powdery mildew effector candidates

2012
PMCID: 3582587
PMID: 23231440
DOI: 10.1186/1471-2164-13-694

[…] amino acid sequence. the intfold server comprises automated methods for fold recognition (intfold-ts), domain prediction (domfold), disorder prediction (disoclust), binding site residue predictions (funfold) and 3d model quality assessment (modfold) [,,]. for each protein, the pdb header files of the top structural templates were scanned for keywords referring to functions, such as rnase, […]


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FunFOLD institution(s)
Laboratoire de genomique et biochimie du metabolisme, Genoscope, Institut de Genomique, Commissariat a l’Energie Atomique et aux Energies Alternatives, Evry, France; UMR 8030 - Genomique Metabolique, Centre National de la Recherche Scientifique, Evry, France; Department de Biologie, Universite d’Evry-Val-d’Essonne, Evry, France; PRES UniverSud Paris, Saint-Aubin, France; School of Biological Sciences, University of Reading, Reading, UK; BioComputing Section, Medical Research Council Harwell, Harwell Oxford, UK; Beamline B23, Diamond Light Source, Didcot, UK
FunFOLD funding source(s)
Supported by Studentship from the University of Reading, MRC Harwell and the Diamond Light Source; the European Union Seventh Framework Programme [FP7/2007-2013] under grant agreement No. [246556].

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