PreDisorder: Ab Initio Sequence-based Prediction of Protein Disordered Regions

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2009 Dec 23

PMID 20025768

Citations 49

Authors

Xin Deng

Jesse Eickholt

Jianlin Cheng

Affiliations

Soon will be listed here.

Abstract

Background: Disordered regions are segments of the protein chain which do not adopt stable structures. Such segments are often of interest because they have a close relationship with protein expression and functionality. As such, protein disorder prediction is important for protein structure prediction, structure determination and function annotation.

Results: This paper presents our protein disorder prediction server, PreDisorder. It is based on our ab initio prediction method (MULTICOM-CMFR) which, along with our meta (or consensus) prediction method (MULTICOM), was recently ranked among the top disorder predictors in the eighth edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP8). We systematically benchmarked PreDisorder along with 26 other protein disorder predictors on the CASP8 data set and assessed its accuracy using a number of measures. The results show that it compared favourably with other ab initio methods and its performance is comparable to that of the best meta and clustering methods.

Conclusion: PreDisorder is a fast and reliable server which can be used to predict protein disordered regions on genomic scale. It is available at http://casp.rnet.missouri.edu/predisorder.html.

Citing Articles

Assessment of Disordered Linker Predictions in the CAID2 Experiment.

Wang K, Hu G, Wu Z, Uversky V, Kurgan L Biomolecules. 2024; 14(3).

PMID: 38540707 PMC: 10968229. DOI: 10.3390/biom14030287.

Protein intrinsically disordered region prediction by combining neural architecture search and multi-objective genetic algorithm.

Tang Y, Yan K, Zhang X, Tian Y, Liu B BMC Biol. 2023; 21(1):188.

PMID: 37674132 PMC: 10483879. DOI: 10.1186/s12915-023-01672-5.

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.

Del Conte A, Bouhraoua A, Mehdiabadi M, Clementel D, Monzon A, Tosatto S Nucleic Acids Res. 2023; 51(W1):W62-W69.

PMID: 37246642 PMC: 10320102. DOI: 10.1093/nar/gkad430.

ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers.

Redl I, Fisicaro C, Dutton O, Hoffmann F, Henderson L, Owens B NAR Genom Bioinform. 2023; 5(2):lqad041.

PMID: 37138579 PMC: 10150328. DOI: 10.1093/nargab/lqad041.

SETH predicts nuances of residue disorder from protein embeddings.

Ilzhofer D, Heinzinger M, Rost B Front Bioinform. 2022; 2:1019597.

PMID: 36304335 PMC: 9580958. DOI: 10.3389/fbinf.2022.1019597.

References

Melamud E, Moult J . Evaluation of disorder predictions in CASP5. Proteins. 2003; 53 Suppl 6:561-5. DOI: 10.1002/prot.10533. View

Kajan L, Rychlewski L . Evaluation of 3D-Jury on CASP7 models. BMC Bioinformatics. 2007; 8:304. PMC: 2040163. DOI: 10.1186/1471-2105-8-304. View

Su C, Chen C, Ou Y . Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics. 2006; 7:319. PMC: 1526762. DOI: 10.1186/1471-2105-7-319. View

Ward J, Sodhi J, McGuffin L, Buxton B, Jones D . Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol. 2004; 337(3):635-45. DOI: 10.1016/j.jmb.2004.02.002. View

Bordoli L, Kiefer F, Schwede T . Assessment of disorder predictions in CASP7. Proteins. 2007; 69 Suppl 8:129-36. DOI: 10.1002/prot.21671. View

Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker A . Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins. 2005; 61 Suppl 7:176-182. DOI: 10.1002/prot.20735. View

Cheng J, Randall A, Sweredoski M, Baldi P . SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005; 33(Web Server issue):W72-6. PMC: 1160157. DOI: 10.1093/nar/gki396. View

Dunker A, Obradovic Z . The protein trinity--linking function and disorder. Nat Biotechnol. 2001; 19(9):805-6. DOI: 10.1038/nbt0901-805. View

Hecker J, Yang J, Cheng J . Protein disorder prediction at multiple levels of sensitivity and specificity. BMC Genomics. 2008; 9 Suppl 1:S9. PMC: 2386074. DOI: 10.1186/1471-2164-9-S1-S9. View

10.

Ward J, McGuffin L, Bryson K, Buxton B, Jones D . The DISOPRED server for the prediction of protein disorder. Bioinformatics. 2004; 20(13):2138-9. DOI: 10.1093/bioinformatics/bth195. View

11.

Coeytaux K, Poupon A . Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics. 2005; 21(9):1891-900. DOI: 10.1093/bioinformatics/bti266. View

12.

Dunker A, Brown C, Lawson J, Iakoucheva L, Obradovic Z . Intrinsic disorder and protein function. Biochemistry. 2002; 41(21):6573-82. DOI: 10.1021/bi012159+. View

13.

Ferron F, Longhi S, Canard B, Karlin D . A practical overview of protein disorder prediction methods. Proteins. 2006; 65(1):1-14. DOI: 10.1002/prot.21075. View

14.

Dyson H, Wright P . Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol. 2005; 6(3):197-208. DOI: 10.1038/nrm1589. View

15.

Ginalski K, Elofsson A, Fischer D, Rychlewski L . 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 2003; 19(8):1015-8. DOI: 10.1093/bioinformatics/btg124. View

16.

Pollastri G, Baldi P, Fariselli P, Casadio R . Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 2002; 47(2):142-53. DOI: 10.1002/prot.10069. View

17.

Mohan A, Uversky V, Radivojac P . Influence of sequence changes and environment on intrinsically disordered proteins. PLoS Comput Biol. 2009; 5(9):e1000497. PMC: 2727479. DOI: 10.1371/journal.pcbi.1000497. View

18.

Noivirt-Brik O, Prilusky J, Sussman J . Assessment of disorder predictions in CASP8. Proteins. 2009; 77 Suppl 9:210-6. DOI: 10.1002/prot.22586. View

19.

McGuffin L . Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics. 2008; 24(16):1798-804. DOI: 10.1093/bioinformatics/btn326. View

20.

Vullo A, Bortolami O, Pollastri G, Tosatto S . Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 2006; 34(Web Server issue):W164-8. PMC: 1538873. DOI: 10.1093/nar/gkl166. View