IDRPred

IDRPred is a modern implementation of MobiDB-lite[1], a method for identifying intrinsically disordered regions (IDRs) in proteins. MobiDB-lite uses multiple predictors to derive a consensus, which is filtered for spurious short predictions in a second step.

The main advantage of IDRPred is that it only requires Python 3 while MobiDB-lite requires both Python 2 and 3.

Installation

pip install git+https://github.com/matthiasblum/idrpred

Docker

A Docker image of idrpred is available from Docker Hub.

Usage

idrpred [options] [infile] [outfile]

Positional arguments:

• infile: The FASTA file of sequences to process. If - or not specified, read from standard input.
• outfile: The TSV file of predicted intrinsically disordered regions. If - or not specified, write to standard output.

Available options

Options	Description
--force	Derive a consensus as long as one predictor did not fail
--skip-features	Do not indentify sequence features, such as domains of low complexity
--round	Round scores reported by individual predictors, like MobiDB-lite does
--tempdir PATH	Create temporary files in PATH, instead of the default temporary directory (most likely /tmp)
--threads N	Process up to N sequences concurrently, default: 1

Predictors

Only predictors whose licence authorises distribution have been included in IDRPred.

Method	Reference	Available
ANCHOR	[2]	❌
DisEMBL-465	[3]	✔
DisEMBL-HotLoops	[3]	✔
DynaMine	[4]	❌
ESpritz-DisProt	[5]	✔
ESpritz-NMR	[5]	✔
ESpritz-Xray	[5]	✔
FeSS	[6]	❌
GlobPlot	[7]	✔
IUPred-Long	[8]	✔
IUPred-Short	[8]	✔
JRONN	[9]	❌
Pfilt	[10]	❌
SEG	[11]	✔
VSL2b	[12]	❌

Comparison

Annotations

Reference proteome	Sequences	Default options	IDRPred: --round option
A. thaliana	39,320
D. melanogaster	26,706
E. Coli	4,403
H. Sapiens	82,492
S. cerevisiae	6,060

Performances

Single-threaded

Wall clock time to annotate common proteomes using one thread:

Multithreaded

Wall clock time to annotate common proteomes using eight threads:

Wall clock time to annotate one million sequences randomly selected from UniParc using sixteen threads:

References

1. Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE. MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins. Bioinformatics. 2021 Apr 1;36(22-23):5533-5534. DOI: 10.1093/bioinformatics/btaa1045. PMID: 33325498.
2. Dosztányi Z, Mészáros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009 Oct 15;25(20):2745-6. DOI: 10.1093/bioinformatics/btp518. Epub 2009 Aug 28. PMID: 19717576; PMCID: PMC2759549.
3. Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure. 2003 Nov;11(11):1453-9. DOI: 10.1016/j.str.2003.10.002. PMID: 14604535.
4. Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. From protein sequence to dynamics and disorder with DynaMine. Nat Commun. 2013;4:2741. DOI: 10.1038/ncomms3741. PMID: 24225580.
5. Walsh I, Martin AJ, Di Domenico T, Tosatto SC. ESpritz: accurate and fast prediction of protein disorder. Bioinformatics. 2012 Feb 15;28(4):503-9. DOI: 10.1093/bioinformatics/btr682. Epub 2011 Dec 20. PMID: 22190692.
6. Piovesan D, Walsh I, Minervini G, Tosatto SCE. FELLS: fast estimator of latent local structure. Bioinformatics. 2017 Jun 15;33(12):1889-1891. DOI: 10.1093/bioinformatics/btx085. PMID: 28186245.
7. Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 2003 Jul 1;31(13):3701-8. DOI: 10.1093/nar/gkg519. PMID: 12824398; PMCID: PMC169197.
8. Mészáros B, Erdos G, Dosztányi Z. IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 2018 Jul 2;46(W1):W329-W337. DOI: 10.1093/nar/gky384. PMID: 29860432; PMCID: PMC6030935.
9. Yang ZR, Thomson R, McNeil P, Esnouf RM. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics. 2005 Aug 15;21(16):3369-76. DOI: 10.1093/bioinformatics/bti534. Epub 2005 Jun 9. PMID: 15947016.
10. Jones DT, Swindells MB. Getting the most from PSI-BLAST. Trends Biochem Sci. 2002 Mar;27(3):161-4. DOI: 10.1016/s0968-0004(01)02039-4. PMID: 11893514.
11. Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem. 1994 Sep;18(3):269-85. DOI: 10.1016/0097-8485(94)85023-2. PMID: 7952898.
12. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics. 2006 Apr 17;7:208. DOI: 10.1186/1471-2105-7-208. PMID: 16618368; PMCID: PMC1479845.