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List of disorder prediction software
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<h2 id="external-links">External links</h2> <ul><li><a href="http://iimcb.genesilico.pl/metadisorder/list_of_protein_disorder_tools_programs.html">Curated list of ~40 disorder prediction programs</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Ferron F, Longhi S, Canard B, Karlin D (October 2006). "A practical overview of protein disorder prediction methods". Proteins. 65 (1): 1–14. doi:10.1002/prot.21075. PMID 16856179. S2CID 30231497. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Yang, J; Cheng, WX; Zhao, XF; Wu, G; Sheng, ST; Hu, Q; Ge, H; Qin, Q; Jin, X; Zhang, L; Zhang, P (Nov 2020). "Comprehensive folding variations for protein folding". Proteins: Structure, Function, and Bioinformatics. 90 (11): 1851–1872. doi:10.1002/prot.26381. PMID 35514069. <a href="https://doi.org/10.1002%2Fprot.26381" target="_blank">https://doi.org/10.1002%2Fprot.26381</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Hanson, Jack; Paliwal, Kuldip K.; Litfin, Thomas; Zhou, Yaoqi (2020-03-13). "SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning". Genomics, Proteomics & Bioinformatics. 17 (6): 645–656. doi:10.1016/j.gpb.2019.01.004. ISSN 1672-0229. PMC 7212484. PMID 32173600. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212484" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212484</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia (8 January 2020). "DisProt: intrinsic protein disorder annotation in 2020". Nucleic Acids Research. 48 (D1): D269 – D276. doi:10.1093/nar/gkz975. ISSN 1362-4962. PMC 7145575. PMID 31713636. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145575" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145575</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Soenderby CK, Sommer M, Otto A, Winther O, Nielsen M, Petersen B, Marcatili P (2019). "NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning". Proteins: Structure, Function, and Bioinformatics. 87 (6): 520–527. doi:10.1002/prot.25674. PMID 30785653. S2CID 216629401. <a href="https://semanticscholar.org/paper/a6dfca71fdda41542538d66bfa1f2675ebe1a8e5" target="_blank">https://semanticscholar.org/paper/a6dfca71fdda41542538d66bfa1f2675ebe1a8e5</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Hanson J, Paliwal K, Zhou Y (2018). "Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures". Journal of Chemical Information and Modeling. 58 (11): 2369–2376. doi:10.1021/acs.jcim.8b00636. hdl:10072/382201. PMID 30395465. S2CID 53235372. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Necci, Marco; Piovesan, Damiano; Dosztányi, Zsuzsanna; Tosatto, Silvio C.E. (2017-01-18). "MobiDB-lite: Fast and highly specific consensus prediction of intrinsic disorder in proteins" (PDF). Bioinformatics. 33 (9): 1402–1404. doi:10.1093/bioinformatics/btx015. ISSN 1367-4803. PMID 28453683. <a href="https://www.openaccessrepository.it/record/100837/files/fulltext.pdf" target="_blank">https://www.openaccessrepository.it/record/100837/files/fulltext.pdf</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Hanson J, Yang Y, Paliwal K, Zhou Y (2016). "Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks". Bioinformatics. 33 (5): 685–692. doi:10.1093/bioinformatics/btw678. PMID 28011771. <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtw678" target="_blank">https://doi.org/10.1093%2Fbioinformatics%2Fbtw678</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (March 2004). "Prediction and functional analysis of native disorder in proteins from the three kingdoms of life". J. Mol. Biol. 337 (3): 635–45. CiteSeerX 10.1.1.120.5605. doi:10.1016/j.jmb.2004.02.002. PMID 15019783. <a href="/wiki/CiteSeerX_(identifier)" target="_blank">/wiki/CiteSeerX_(identifier)</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Sormanni P, Camilloni C, Fariselli P, Vendruscolo M (February 2015). "The s2D Method: Simultaneous Sequence- Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins". J. Mol. Biol. 427 (4): 982–996. doi:10.1016/j.jmb.2014.12.007. PMID 25534081. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Sumaiya Iqbal; Md Tamjidul Hoque (October 2015). "DisPredict: A Predictor of Disordered Protein using Optimized RBF Kernel, content and profiles". PLOS ONE. 10 (10): e0141551. doi:10.1371/journal.pone.0141551. PMC 4627842. PMID 26517719. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627842" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627842</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Peng Z, Mizianty MJ, Kurgan L (Jan 2014). "Genome-scale prediction of proteins with long intrinsically disordered regions". Proteins. 82 (1): 145–58. doi:10.1002/prot.24348. PMID 23798504. S2CID 21229963. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Marcin J. Miziantya, Zhenling Penga & Lukasz Kurgan (April 2013). "Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles". Intrinsically Disordered Proteins. 1 (1): e24428. doi:10.4161/idp.24428. PMC 5424793. PMID 28516009. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424793" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5424793</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Kozlowski, L. P.; Bujnicki, J. M. (2012). "MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins". BMC Bioinformatics. 13: 111. doi:10.1186/1471-2105-13-111. PMC 3465245. PMID 22624656. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465245" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465245</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Zhang T, Faraggi E, Xue B, Dunker K, Uversky VN, Zhou Y (February 2012). "SPINE-D: Accurate prediction of short and long disordered regions by a single neural-network based method" (PDF). Journal of Biomolecular Structure and Dynamics. 29 (4): 799–813. doi:10.1080/073911012010525022. hdl:10072/57573. PMC 3297974. PMID 22208280. Archived from the original on November 3, 2013. <a href="https://web.archive.org/web/20131103083554/http://www.jbsdonline.com/mc_images/category/4317/32-keith_dunker_jbsd_29_4.pdf" target="_blank">https://web.archive.org/web/20131103083554/http://www.jbsdonline.com/mc_images/category/4317/32-keith_dunker_jbsd_29_4.pdf</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Mizianty MJ, Stach W, Chen K, Kedarisetti KD, Disfani FM, Kurgan L (September 2010). "Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources". Bioinformatics. 26 (18): i489–96. doi:10.1093/bioinformatics/btq373. PMC 2935446. PMID 20823312. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935446" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935446</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Prilusky J, Felder CE, Zeev-Ben-Mordehai T, et al. (August 2005). "FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded" (PDF). Bioinformatics. 21 (16): 3435–8. doi:10.1093/bioinformatics/bti537. PMID 15955783. <a href="https://serval.unil.ch/resource/serval:BIB_072223A553B5.P001/REF.pdf" target="_blank">https://serval.unil.ch/resource/serval:BIB_072223A553B5.P001/REF.pdf</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Wang L, Sauer UH (June 2008). "OnD-CRF: predicting order and disorder in proteins using conditional random fields". Bioinformatics. 24 (11): 1401–2. doi:10.1093/bioinformatics/btn132. PMC 2387219. PMID 18430742. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387219" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387219</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B (2009). Orgel JP (ed.). "Improved disorder prediction by combination of orthogonal approaches". PLOS ONE. 4 (2): e4433. Bibcode:2009PLoSO...4.4433S. doi:10.1371/journal.pone.0004433. PMC 2635965. PMID 19209228. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635965" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635965</a> <a href="#fnref:19" class="footnote-back-ref">↩</a></p></li> <li id="fn:20"><p>Lieutaud P, Canard B, Longhi S (September 2008). "MeDor: a metaserver for predicting protein disorder". BMC Genomics. 16 (Suppl 2): S25. doi:10.1186/1471-2164-9-S2-S25. PMC 2559890. PMID 18831791. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559890" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559890</a> <a href="#fnref:20" class="footnote-back-ref">↩</a></p></li> </ol>