FunFOLD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FunFOLD

Tool usage distribution map

This map represents all the scientific publications referring to FunFOLD per scientific context
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FunFOLD specifications


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




  • person_outline Liam J. McGuffin
  • person_outline Daniel Roche

Additional information

Publications for FunFOLD

FunFOLD citations


Normal Modes Expose Active Sites in Enzymes

PLoS Comput Biol
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] developed [–]. 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 of the […]


Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

Int J Mol Sci
PMCID: 4691145
PMID: 26694353
DOI: 10.3390/ijms161226202

[…] tional annotation. Furthermore, a number of structure-based methods for the prediction of protein–ligand binding sites have incorporated methods for predicting GO and EC terms, including COACH [] and FunFOLD3 [,,] (See ). However, as these methods build 3D models as part of their prediction pipeline, they are somewhat more computationally intensive than the sequence-only methods. The prediction of […]


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

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

[…] sphatases []. 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. 4Comparing structures of HmsMRE11 (Homo sapiens, PDB : 3T1I) [], PfMRE11 (Pyrococcus furiosus, archaea PDB ID: 1II7, []), Sp MRE11 (Schizosaccharo […]


Hairpins under tension: RNA versus DNA

Nucleic Acids Res
PMCID: 4787782
PMID: 26323319
DOI: 10.1093/nar/gkv860

[…] olution of these probabilities. To obtain the experimental hysteresis distributions, for each molecule the unfolding and folding forces measured are paired to generate all possible hysteresis values (Funfold − Ffold). The obtained values are weighted according to the number of force cycles actually performed on the molecule, and normalized. More details about the building of the histograms are pre […]


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

PLoS One
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. For instanc […]


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

PLoS Comput Biol
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 those […]

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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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