Einzeltreffer — DigiBib

The isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pKa) of charged groups of seven amino acids and NH+ and COO- groups at polypeptide termini. Information regarding isoelectric point and pKa is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry. Therefore, there is a strong need for the in silico prediction of isoelectric point and pKa values. In this paper, I present Isoelectric Point Calculator 2.0 (IPC 2.0), a web server for the prediction of isoelectric points and pKa values using a mixture of deep learning and support vector regression models. The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms: 0.848 versus 0.868 and 0.222 versus 0.405, respectively. Moreover, the IPC 2.0 prediction of pKa using sequence information alone was better than the prediction from structure-based methods (0.576 versus 0.826) and a few folds faster. The IPC 2.0 webserver is freely available at www.ipc2-isoelectric-point.org.

Titel:	IPC 2.0: prediction of isoelectric point and pKa dissociation constants.
Autor/in / Beteiligte Person:	Kozlowski, LP
Link:	Full Text Finder (Volltext)
Zeitschrift:	Nucleic acids research, Jg. 49 (2021-07-02), Heft W1, S. W285-W292
Veröffentlichung:	1992- : Oxford : Oxford University Press ; <i>Original Publication</i>: London, Information Retrieval ltd., 2021
Medientyp:	academicJournal
ISSN:	1362-4962 (electronic)
DOI:	10.1093/nar/gkab295
Schlagwort:	Deep Learning Sequence Analysis, Protein Support Vector Machine Isoelectric Point Peptides chemistry Proteins chemistry Software
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article; Research Support, Non-U.S. Gov't Language: English [Nucleic Acids Res] 2021 Jul 02; Vol. 49 (W1), pp. W285-W292. MeSH Terms: Isoelectric Point* ; Software* ; Peptides / chemistry ; Proteins / chemistry ; Deep Learning ; Sequence Analysis, Protein ; Support Vector Machine References: Anal Biochem. 1989 Jun;179(2):319-25. (PMID: 2774179) ; Elife. 2017 Nov 20;6:. (PMID: 29154755) ; Bioinformatics. 2015 May 1;31(9):1444-51. (PMID: 25573921) ; Trends Genet. 2000 Jun;16(6):276-7. (PMID: 10827456) ; Nat Methods. 2020 Mar;17(3):261-272. (PMID: 32015543) ; Biophys J. 2012 Aug 8;103(3):587-595. (PMID: 22947875) ; Comput Methods Programs Biomed. 2018 Jan;153:1-9. (PMID: 29157442) ; J Comput Chem. 2009 Nov 15;30(14):2231-47. (PMID: 19274707) ; Anal Biochem. 1982 Jan 15;119(2):440-9. (PMID: 7072964) ; Methods Mol Biol. 1999;112:531-52. (PMID: 10027275) ; Nucleic Acids Res. 2012 Jul;40(Web Server issue):W537-41. (PMID: 22570416) ; J Proteome Res. 2013 Feb 1;12(2):1014-9. (PMID: 23214937) ; Nucleic Acids Res. 2008 Jan;36(Database issue):D202-5. (PMID: 17998252) ; Proteomics. 2004 Aug;4(8):2352-6. (PMID: 15274128) ; J Biol Chem. 2009 May 15;284(20):13285-9. (PMID: 19164280) ; Biomed Khim. 2015 Jan-Feb;61(1):83-91. (PMID: 25762601) ; J Am Soc Mass Spectrom. 2010 Sep;21(9):1612-9. (PMID: 20537905) ; BMC Struct Biol. 2011 Jan 26;11:6. (PMID: 21269479) ; J Biol Chem. 1975 May 25;250(10):4007-21. (PMID: 236308) ; Protein Sci. 2009 Jan;18(1):247-51. (PMID: 19177368) ; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W638-44. (PMID: 15215467) ; Nat Methods. 2014 Jan;11(1):59-62. (PMID: 24240322) ; J Biol Chem. 1971 Apr 10;246(7):2211-7. (PMID: 5555568) ; Electrophoresis. 2008 Jul;29(13):2768-78. (PMID: 18615785) ; PLoS Pathog. 2019 Jun 26;15(6):e1007828. (PMID: 31242261) ; Protein Sci. 2006 May;15(5):1214-8. (PMID: 16597822) ; Electrophoresis. 1994 Mar-Apr;15(3-4):529-39. (PMID: 8055880) ; Database (Oxford). 2019 Jan 1;2019:. (PMID: 30805645) ; Proteomics. 2008 Dec;8(23-24):4898-906. (PMID: 19003858) ; Humangenetik. 1975;26(3):231-43. (PMID: 1093965) ; J Proteomics. 2012 Apr 3;75(7):2269-74. (PMID: 22326964) ; Nat Commun. 2019 Apr 8;10(1):1600. (PMID: 30962452) ; J Proteome Res. 2002 Jan-Feb;1(1):21-6. (PMID: 12643522) ; Genome Biol. 2018 Jun 7;19(1):75. (PMID: 29880023) ; Nucleic Acids Res. 2017 Jan 4;45(D1):D1112-D1116. (PMID: 27789699) ; J Proteome Res. 2005 Nov-Dec;4(6):2273-82. (PMID: 16335976) ; Bioinformatics. 2015 Jan 15;31(2):295-6. (PMID: 25252779) ; Nucleic Acids Res. 2006 Jan 1;34(Database issue):D199-203. (PMID: 16381845) ; Biol Direct. 2016 Oct 21;11(1):55. (PMID: 27769290) ; Anal Biochem. 1995 Oct 10;231(1):82-91. (PMID: 8678324) Substance Nomenclature: 0 (Peptides) ; 0 (Proteins) Entry Date(s): Date Created: 20210427 Date Completed: 20210714 Latest Revision: 20210714 Update Code: 20231215 PubMed Central ID: PMC8262712

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IPC 2.0: prediction of isoelectric point and pKa dissociation constants.