A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, 2011-

Deep Learning* ; Proteins*/chemistry ; Protein Structure, Quaternary*; Models, Molecular ; Humans

The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them appropriately in biomedical research, such as protein-protein interaction studies, protein design, and drug discovery. With the advent of more accurate protein complex (multimer) prediction tools, such as AlphaFold2-Multimer and ESMFold, the estimation of the accuracy of protein complex structures has attracted increasing attention. Many deep learning methods have been developed to tackle this problem; however, there is a noticeable absence of a comprehensive overview of these methods to facilitate future development. Addressing this gap, we present a review of deep learning EMA methods for protein complex structures developed in the past several years, analyzing their methodologies, data and feature construction. We also provide a prospective summary of some potential new developments for further improving the accuracy of the EMA methods.

Bioinformatics. 2016 Jun 15;32(12):i262-i270. (PMID: 27307625)
Brief Bioinform. 2023 Nov 22;25(1):. (PMID: 38018909)
Proteins. 2007 Jun 1;67(4):1078-86. (PMID: 17373710)
Protein Sci. 2024 Mar;33(3):e4932. (PMID: 38380738)
Proteins. 2023 Dec;91(12):1850-1860. (PMID: 37858934)
Proteins. 2023 Dec;91(12):1889-1902. (PMID: 37357816)
Proteins. 2021 May;89(5):493-501. (PMID: 33289162)
Molecules. 2018 Aug 06;23(8):. (PMID: 30082644)
Bioinform Adv. 2021 Dec 10;2(1):vbab042. (PMID: 36699405)
Science. 2023 Mar 17;379(6637):1123-1130. (PMID: 36927031)
Nat Commun. 2022 Mar 10;13(1):1265. (PMID: 35273146)
Curr Opin Biotechnol. 2007 Aug;18(4):305-11. (PMID: 17644370)
Curr Drug Metab. 2017;18(1):5-10. (PMID: 28889796)
Sci Rep. 2017 Sep 5;7(1):10480. (PMID: 28874689)
Bioinformatics. 2023 Jan 1;39(1):. (PMID: 36637199)
Brief Bioinform. 2023 Jan 19;24(1):. (PMID: 36460624)
Proteins. 2023 Dec;91(12):1861-1870. (PMID: 37553848)
Science. 2021 Aug 20;373(6557):871-876. (PMID: 34282049)
Proteins. 2023 Dec;91(12):1879-1888. (PMID: 37482904)
PLoS One. 2016 Aug 25;11(8):e0161879. (PMID: 27560519)
Bioinformatics. 2020 Apr 1;36(7):2113-2118. (PMID: 31746961)
Proteins. 2010 Nov 15;78(15):3111-4. (PMID: 20806234)
Bioinform Adv. 2023 Jun 02;3(1):vbad070. (PMID: 37351310)
Methods Enzymol. 2011;487:545-74. (PMID: 21187238)
Front Mol Biosci. 2021 May 25;8:647915. (PMID: 34113650)
Proteins. 2004 Dec 1;57(4):702-10. (PMID: 15476259)
Proteins. 2020 Aug;88(8):1091-1099. (PMID: 32144844)
IEEE/ACM Trans Comput Biol Bioinform. 2023 Sep-Oct;20(5):3128-3138. (PMID: 37220029)
Nucleic Acids Res. 2003 Jul 1;31(13):3370-4. (PMID: 12824330)
Bioinformatics. 2020 Jun 1;36(12):3758-3765. (PMID: 32259206)
Bioinform Adv. 2023 Feb 03;3(1):vbad011. (PMID: 36818727)
Methods Mol Biol. 2024;2714:101-112. (PMID: 37676594)
Bioinformatics. 2017 Jun 15;33(12):1806-1813. (PMID: 28200016)
Proteins. 2023 Dec;91(12):1658-1683. (PMID: 37905971)
Proteins. 2008 Aug;72(2):557-79. (PMID: 18247354)
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. (PMID: 18442991)
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W310-4. (PMID: 16845016)
Biophys J. 2011 Oct 19;101(8):2043-52. (PMID: 22004759)
Nucleic Acids Res. 2022 Jan 7;50(D1):D439-D444. (PMID: 34791371)
Bioinformatics. 2020 Jan 1;36(1):112-121. (PMID: 31199455)
Proteins. 2005 Aug 1;60(2):296-301. (PMID: 15981259)
Proteins. 2017 Mar;85(3):417-423. (PMID: 27802573)
Bioinformatics. 2008 Nov 15;24(22):2634-5. (PMID: 18812365)
Proteins. 2013 Jan;81(1):149-62. (PMID: 22933340)
Protein Sci. 2011 Sep;20(9):1576-86. (PMID: 21739500)
Proteins. 2000 Jan 1;38(1):3-16. (PMID: 10651034)
Proteins. 2001 Aug 15;44(3):223-32. (PMID: 11455595)
Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i308-i317. (PMID: 37387159)
Bioinformatics. 2024 Feb 1;40(2):. (PMID: 38373819)
J Mol Biol. 1997 Sep 12;272(1):106-20. (PMID: 9299341)
Bioinformatics. 2013 Nov 1;29(21):2722-8. (PMID: 23986568)
Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):459-63. (PMID: 16524834)
J Mol Biol. 2015 Sep 25;427(19):3031-41. (PMID: 26231283)
Brief Bioinform. 2023 Sep 22;24(6):. (PMID: 37930021)
Proteins. 2023 Dec;91(12):1871-1878. (PMID: 37314190)
Bioinformatics. 2014 Jun 15;30(12):1771-3. (PMID: 24532726)
Front Bioinform. 2021 Aug 12;1:693211. (PMID: 36303780)
Nat Commun. 2021 Dec 3;12(1):7068. (PMID: 34862392)
Bioinformatics. 2022 Apr 28;38(9):2444-2451. (PMID: 35199137)
Proteins. 2003 Jul 1;52(1):88-91. (PMID: 12784372)
Bioinformatics. 2016 Dec 15;32(24):3760-3767. (PMID: 27551106)
Bioinformatics. 2023 Oct 3;39(10):. (PMID: 37740296)
Bioinformatics. 2022 Mar 28;38(7):1895-1903. (PMID: 35134108)
Proteins. 2008 Jul;72(1):270-9. (PMID: 18214977)
Bioinformatics. 2023 Jan 1;39(1):. (PMID: 36420989)
Nat Rev Drug Discov. 2016 Aug;15(8):533-50. (PMID: 27050677)
Proteins. 2014 Nov;82(11):3163-9. (PMID: 25179222)
Bioinformatics. 2013 Mar 15;29(6):807-9. (PMID: 23343604)
Brief Bioinform. 2023 Jul 20;24(4):. (PMID: 37317619)
J Am Chem Soc. 2003 Feb 19;125(7):1731-7. (PMID: 12580598)

R01GM093123 and R01GM146340 United States NH NIH HHS

Keywords: deep learning; estimation of model accuracy; protein complex; protein quality assessment; protein quaternary structure

0 (Proteins)

Date Created: 20240524 Date Completed: 20240524 Latest Revision: 20240610

20240611

PMC11117562

10.3390/biom14050574

38785981