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IntFOLD

From EverybodyWiki Bios & Wiki



The IntFOLD server
Developer(s)Prof Liam McGuffin

Dr Recep Adiyaman

Dr Bajuna Salehe
Stable release
IntFOLD version 5.0
Preview release
IntFOLD version 6.0
Written inJava,

Python,

R
Engine
    Websitehttps://www.reading.ac.uk/bioinf/IntFOLD/

    Search IntFOLD on Amazon.

    (A) The output page showing the results (from top to bottom): 1. The top 5 3D models ranked by ModFOLD global scores (table truncated here to fit); 2. The predicted unstructured/disordered regions for the top 3D model; 3. The predicted structural domain boundaries; 4. The predicted ligand-binding site; 5. The rankings for all generated models (table truncated here to fit). The arrows point to additional pages that are linked to when users click on images/buttons on the main page. (B) After clicking the button of ‘View model in 3D and download’ shows the interactive page of the model, and 3D superpositions of the model with related template/s, which can be visualised by using the JSmol/HTML5 framework (http://www.jmol.org/). (C) Clicking the button of ‘Refine model using ReFOLD’ submits the 3D model to the ReFOLD sever (21) for the refinement of the 3D model. (D) Clicking on the image of the ligand-binding site prediction leads to the page that provides the information about the predicted protein-ligand binding site with JSmol.
    Figure 1. The IntFOLD5 results pages for the CASP13 (T0961) target

    IntFOLD is a freely available an integrated protein structure and function prediction server developed in the UK[1]. The server is unique in providing a unified interface for: tertiary structure prediction/3D modelling, 3D model quality estimates, intrinsic disorder prediction, domain prediction and prediction of protein-ligand binding residues. It now also includes the option to refine/fix errors using the ReFOLD3 method [2].

    Description

    The underlying guiding principle of IntFOLD method is that model quality assessment (QA) is a key step for homology modelling. The method originates from the IntFOLD-TS method[3], which firstly generates numerous alternate models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing QA method—ModFOLD8 [4]. IntFOLD server provides the tertiary structure prediction at a competitive accuracy and combines the cutting edge methods including IntFOLD-TS for generation of 3D models [5][1][6][7], ModFOLD for 3D model quality estimation [5][8], ReFOLD for refinement of 3D models [2], DISOclust for disorder prediction [9][10] , DomFOLD for structural domain prediction [6][7] , and FunFOLD for protein ligand binding site prediction [11][12]. The integration of the tools enables users to reach all related information in a pipeline. IntFOLD Web Server has completed over ∼200 000 structure predictions since  January 2010 [1]. IntFOLD server is freely available at http://www.reading.ac.uk/bioinf/IntFOLD/.

    The only required input is a protein sequence for the prediction of the protein 3D structure and function [1]. The IntFOLD output is presented via a user-friendly interface, plots and annotated theoretical 3D models for the use of life scientists, as shown in Figure 1 . The raw data is also formatted in Critical Assessment of Methods for Protein Structure Prediction (CASP) standards with a detailed help page [1].

    Performance in CASP and CAMEO experiments

    The IntFOLD method was firstly benchmarked in Critical Assessment of Techniques for Protein Structure Prediction 9 (CASP9) and ranked among the top 5.[6]. The IntFOLD server has consolidated its performance in the following CASP experiments [1][7][6]

    Its performance is being continually evaluated in Continuous Automated Model EvaluatiOn (CAMEO) experiment. The performance summary of successive IntFOLD versions have ranked among top independent servers [1].

    Applications of IntFOLD server

    Recently, IntFOLD was used to generate the 3D models for the SARS-CoV-2 targets for the CASP Commons COVID-19 initiative.[2][13]. Different structures related to novel proteins in the Drosophila melanogaster genome [14], mammalian GCKIII kinases [15][16] , Pseudomonas fluorescens [17], proteome of barley powdery mildew (Blumeria graminis f. sp. hordei) [18], and dermatosparaxis [19] were also investigated [1]


    References

    1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 McGuffin, Liam J; Adiyaman, Recep; Maghrabi, Ali H A; Shuid, Ahmad N; Brackenridge, Danielle A; Nealon, John O; Philomina, Limcy S (2019-05-02). "IntFOLD: an integrated web resource for high performance protein structure and function prediction". Nucleic Acids Research. 47 (W1): W408–W413. doi:10.1093/nar/gkz322. ISSN 0305-1048. PMC 6602432 Check |pmc= value (help). PMID 31045208.
    2. ↑ 2.0 2.1 2.2 Adiyaman, Recep; McGuffin, Liam J (2021-05-01). "ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts". Nucleic Acids Research. 49 (W1): W589–W596. doi:10.1093/nar/gkab300. ISSN 0305-1048. PMC 8218204 Check |pmc= value (help). PMID 34009387 Check |pmid= value (help).
    3. ↑ McGuffin, Liam J.; Roche, Daniel B. (2011). "Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method". Proteins: Structure, Function, and Bioinformatics. 79 (S10): 137–146. doi:10.1002/prot.23120. ISSN 1097-0134. PMID 22069035. Unknown parameter |s2cid= ignored (help)
    4. ↑ McGuffin, Liam J; Aldowsari, Fahd M F; Alharbi, Shuaa M A; Adiyaman, Recep (2021-05-08). "ModFOLD8: accurate global and local quality estimates for 3D protein models". Nucleic Acids Research. 49 (W1): W425–W430. doi:10.1093/nar/gkab321. ISSN 0305-1048. PMC 8218196 Check |pmc= value (help). PMID 33963867 Check |pmid= value (help).
    5. ↑ 5.0 5.1 McGuffin, Liam J.; Shuid, Ahmad N.; Kempster, Robert; Maghrabi, Ali H.A.; Nealon, John O.; Salehe, Bajuna R.; Atkins, Jennifer D.; Roche, Daniel B. (2017-08-08). "Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods". Proteins: Structure, Function, and Bioinformatics. 86: 335–344. doi:10.1002/prot.25360. ISSN 0887-3585. PMID 28748648. Unknown parameter |s2cid= ignored (help)
    6. ↑ 6.0 6.1 6.2 6.3 Roche, D. B.; Buenavista, M. T.; Tetchner, S. J.; McGuffin, L. J. (2011-03-31). "The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction". Nucleic Acids Research. 39 (suppl): W171–W176. doi:10.1093/nar/gkr184. ISSN 0305-1048. PMC 3125722. PMID 21459847.
    7. ↑ 7.0 7.1 7.2 McGuffin, Liam J.; Atkins, Jennifer D.; Salehe, Bajuna R.; Shuid, Ahmad N.; Roche, Daniel B. (2015-03-27). "IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1". Nucleic Acids Research. 43 (W1): W169–W173. doi:10.1093/nar/gkv236. ISSN 0305-1048. PMC 4489238. PMID 25820431.
    8. ↑ Maghrabi, Ali H. A.; McGuffin, Liam J. (2017-04-29). "ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models". Nucleic Acids Research. 45 (W1): W416–W421. doi:10.1093/nar/gkx332. ISSN 0305-1048. PMC 5570241. PMID 28460136.
    9. ↑ Atkins, Jennifer; Boateng, Samuel; Sorensen, Thomas; McGuffin, Liam (2015-08-13). "Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies". International Journal of Molecular Sciences. 16 (8): 19040–19054. doi:10.3390/ijms160819040. ISSN 1422-0067. PMC 4581285. PMID 26287166.
    10. ↑ McGuffin, Liam J. (2008-08-15). "Intrinsic disorder prediction from the analysis of multiple protein fold recognition models". Bioinformatics. 24 (16): 1798–1804. doi:10.1093/bioinformatics/btn326. ISSN 1367-4803. PMID 18579567.
    11. ↑ Roche, Daniel B; Tetchner, Stuart J; McGuffin, Liam J (2011). "FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins". BMC Bioinformatics. 12 (1): 160. doi:10.1186/1471-2105-12-160. ISSN 1471-2105. PMC 3123233. PMID 21575183.
    12. ↑ Roche, Daniel B.; Buenavista, Maria T.; McGuffin, Liam J. (2013-06-11). "The FunFOLD2 server for the prediction of protein–ligand interactions". Nucleic Acids Research. 41 (W1): W303–W307. doi:10.1093/nar/gkt498. ISSN 1362-4962. PMC 3692132. PMID 23761453.
    13. ↑ Kryshtafovych, Andriy; Moult, John; Billings, Wendy M.; Corte, Dennis Della; Fidelis, Krzysztof; Kwon, Sohee; Olechnovič, Kliment; Seok, Chaok; Venclovas, Česlovas; Won, Jonghun. "Modeling SARS-CoV2 proteins in the CASP-commons experiment". Proteins: Structure, Function, and Bioinformatics. n/a (n/a). doi:10.1002/prot.26231. ISSN 1097-0134.
    14. ↑ Dunwell, Thomas L; McGuffin, Liam J; Dunwell, Jim M; Pfeifer, Gerd P (2013-09-19). "The mysterious presence of a 5-methylcytosine oxidase in theDrosophilagenome". Cell Cycle. 12 (21): 3357–3365. doi:10.4161/cc.26540. ISSN 1538-4101. PMC 3895424. PMID 24091536.
    15. ↑ Fuller, Stephen J.; McGuffin, Liam J.; Marshall, Andrew K.; Giraldo, Alejandro; Pikkarainen, Sampsa; Clerk, Angela; Sugden, Peter H. (2012-02-24). "A novel non-canonical mechanism of regulation of MST3 (mammalian Sterile20-related kinase 3)". Biochemical Journal. 442 (3): 595–610. doi:10.1042/bj20112000. ISSN 0264-6021. PMC 3286863. PMID 22229648.
    16. ↑ Sugden, Peter H.; McGuffin, Liam J.; Clerk, Angela (2013-07-26). "SOcK, MiSTs, MASK and STicKs: the GCKIII (germinal centre kinase III) kinases and their heterologous protein–protein interactions". Biochemical Journal. 454 (1): 13–30. doi:10.1042/bj20130219. ISSN 0264-6021. PMID 23889253.
    17. ↑ W, Taylor, Tiffany B Mulley, Geraldine Dills, Alexander H Alsohim, Abdullah S McGuffin, Liam J Studholme, David J Silby, Mark W Brockhurst, Michael A Johnson, Louise J Jackson, Robert. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. OCLC 971601572. Search this book on
    18. ↑ Bindschedler, Laurence V.; McGuffin, Liam J.; Burgis, Timothy A.; Spanu, Pietro D.; Cramer, Rainer (August 2011). "Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei". Methods. 54 (4): 432–441. doi:10.1016/j.ymeth.2011.03.006. ISSN 1046-2023. PMID 21453771.
    19. ↑ Monteagudo, Luis V.; Ferrer, Luis M.; Catalan-Insa, Elena; Savva, Demetris; McGuffin, Liam J.; Tejedor, Maria T. (2014-10-30). "In silicoidentification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis". Veterinary Dermatology. 26 (1): 49–e16. doi:10.1111/vde.12178. ISSN 0959-4493. PMID 25354687.


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