Molecular Modelling in Bioactive Peptide Discovery and Characterisation.

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-

Peptides*/chemistry ; Models, Molecular*; Molecular Dynamics Simulation ; Deep Learning ; Drug Discovery ; Molecular Docking Simulation ; Protein Conformation ; Humans

Molecular modelling is a vital tool in the discovery and characterisation of bioactive peptides, providing insights into their structural properties and interactions with biological targets. Many models predicting bioactive peptide function or structure rely on their intrinsic properties, including the influence of amino acid composition, sequence, and chain length, which impact stability, folding, aggregation, and target interaction. Homology modelling predicts peptide structures based on known templates. Peptide-protein interactions can be explored using molecular docking techniques, but there are challenges related to the inherent flexibility of peptides, which can be addressed by more computationally intensive approaches that consider their movement over time, called molecular dynamics (MD). Virtual screening of many peptides, usually against a single target, enables rapid identification of potential bioactive peptides from large libraries, typically using docking approaches. The integration of artificial intelligence (AI) has transformed peptide discovery by leveraging large amounts of data. AlphaFold is a general protein structure prediction tool based on deep learning that has greatly improved the predictions of peptide conformations and interactions, in addition to providing estimates of model accuracy at each residue which greatly guide interpretation. Peptide function and structure prediction are being further enhanced using Protein Language Models (PLMs), which are large deep-learning-derived statistical models that learn computer representations useful to identify fundamental patterns of proteins. Recent methodological developments are discussed in the context of canonical peptides, as well as those with modifications and cyclisations. In designing potential peptide therapeutics, the main outstanding challenge for these methods is the incorporation of diverse non-canonical amino acids and cyclisations.

J Chem Phys. 2020 Oct 21;153(15):154109. (PMID: 33092378)
Int J Mol Sci. 2023 Aug 26;24(17):. (PMID: 37686057)
ACS Appl Bio Mater. 2024 Feb 19;7(2):617-625. (PMID: 36971822)
Pharmaceuticals (Basel). 2023 Mar 14;16(3):. (PMID: 36986538)
Science. 2023 Mar 17;379(6637):1123-1130. (PMID: 36927031)
Expert Opin Investig Drugs. 2007 Nov;16(11):1851-63. (PMID: 17970643)
Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3445-54. (PMID: 23946421)
Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4758-E4766. (PMID: 29735687)
J Comput Chem. 2005 Dec;26(16):1668-88. (PMID: 16200636)
J Comput Chem. 2004 Jul 15;25(9):1157-74. (PMID: 15116359)
J Agric Food Chem. 2022 Feb 2;70(4):934-943. (PMID: 34990125)
Nature. 2023 Aug;620(7976):1089-1100. (PMID: 37433327)
Mol Cell Proteomics. 2020 Jul;19(7):1070-1075. (PMID: 32345597)
Chem Biol Drug Des. 2019 Jan;93(1):12-20. (PMID: 30187647)
Curr Res Food Sci. 2022 Nov 05;5:2162-2170. (PMID: 36387592)
J Biomed Nanotechnol. 2020 Dec 1;16(12):1687-1718. (PMID: 33485398)
J Mol Biol. 2008 Sep 12;381(4):1068-87. (PMID: 18640688)
Methods Mol Biol. 2020;2068:129-162. (PMID: 31576526)
ACS Med Chem Lett. 2023 Apr 24;14(5):557-565. (PMID: 37197469)
Eur Biophys J. 2005 Jun;34(4):273-84. (PMID: 15803330)
Curr Opin Struct Biol. 2023 Jun;80:102601. (PMID: 37182397)
Molecules. 2023 Oct 19;28(20):. (PMID: 37894644)
Curr Opin Biotechnol. 2008 Aug;19(4):344-50. (PMID: 18602004)
Molecules. 2022 Sep 14;27(18):. (PMID: 36144718)
PLoS Comput Biol. 2022 Dec 12;18(12):e1010661. (PMID: 36508460)
Proteins. 2023 Dec;91(12):1616-1635. (PMID: 37746927)
Front Microbiol. 2020 Jan 22;10:3097. (PMID: 32038544)
Nat Commun. 2024 Jul 20;15(1):6114. (PMID: 39030199)
Front Nutr. 2024 Nov 14;11:1496706. (PMID: 39610876)
J Cheminform. 2011 Nov 01;3(1):49. (PMID: 22044511)
J Chem Theory Comput. 2013 Jan 8;9(1):834-46. (PMID: 26589074)
Wiley Interdiscip Rev Comput Mol Sci. 2021 Sep-Oct;11(5):. (PMID: 34899998)
Cancer Res. 2017 Nov 1;77(21):e55-e57. (PMID: 29092940)
Sci Rep. 2021 May 20;11(1):10630. (PMID: 34017051)
Chemistry. 2012 Jun 25;18(26):7984-99. (PMID: 22688954)
Interface Focus. 2017 Dec 6;7(6):20170030. (PMID: 29147559)
Structure. 2015 May 5;23(5):929-940. (PMID: 25914054)
Nat Protoc. 2022 Oct;17(10):2326-2353. (PMID: 35931779)
Molecules. 2021 Jan 15;26(2):. (PMID: 33467522)
Biopolymers. 2015 Jul;104(4):360-70. (PMID: 25784456)
Structure. 2023 Jan 5;31(1):111-119.e2. (PMID: 36525975)
Protein Eng Des Sel. 2011 Sep;24(9):635-48. (PMID: 21676899)
Methods Mol Biol. 2015;1215:47-71. (PMID: 25330958)
Biochem Soc Trans. 2020 Aug 28;48(4):1707-1724. (PMID: 32756904)
J Med Chem. 2022 Dec 8;65(23):15819-15839. (PMID: 36442155)
ACS Omega. 2021 Sep 15;6(38):24432-24443. (PMID: 34604625)
Expert Opin Drug Discov. 2015 Dec;10(12):1301-13. (PMID: 26414598)
Annu Rev Phys Chem. 2020 Apr 20;71:361-390. (PMID: 32092281)
Protein Eng. 2000 Aug;13(8):551-5. (PMID: 10964984)
Methods Mol Biol. 2012;819:169-86. (PMID: 22183537)
PLoS One. 2011;6(5):e20044. (PMID: 21625446)
Antibiotics (Basel). 2020 Aug 26;9(9):. (PMID: 32858882)
RSC Chem Biol. 2024 Mar 13;5(5):401-417. (PMID: 38725911)
Commun Chem. 2022 Feb 24;5(1):23. (PMID: 36697632)
Future Med Chem. 2012 Aug;4(12):1619-44. (PMID: 22917249)
Science. 2021 Aug 20;373(6557):871-876. (PMID: 34282049)
Molecules. 2020 Nov 19;25(22):. (PMID: 33227894)
Nucleic Acids Res. 2016 Jul 8;44(W1):W430-5. (PMID: 27112573)
Biomolecules. 2018 Aug 22;8(3):. (PMID: 30135402)
Bioinformatics. 2011 Oct 15;27(20):2836-42. (PMID: 21880702)
Signal Transduct Target Ther. 2025 Mar 5;10(1):74. (PMID: 40038239)
Future Med Chem. 2017 Sep;9(14):1665-1686. (PMID: 28841048)
J Mol Biol. 2005 Nov 18;354(1):173-83. (PMID: 16236315)
Phys Chem Chem Phys. 2019 Oct 9;21(39):21918-21931. (PMID: 31552948)
PLoS One. 2019 May 30;14(5):e0197644. (PMID: 31145747)
Membranes (Basel). 2022 Aug 29;12(9):. (PMID: 36135863)
J Mol Biol. 1997 Apr 4;267(3):727-48. (PMID: 9126849)
Nat Methods. 2022 Jun;19(6):679-682. (PMID: 35637307)
Structure. 2016 Oct 4;24(10):1842-1853. (PMID: 27642160)
PLoS One. 2011 Apr 29;6(4):e18934. (PMID: 21572516)
Adv Biol (Weinh). 2023 Jun;7(6):e2200232. (PMID: 36775876)
Front Genet. 2021 Nov 19;12:768979. (PMID: 34868255)
Int J Mol Sci. 2022 Jan 27;23(3):. (PMID: 35163367)
J Mol Model. 2017 Nov 21;23(12):349. (PMID: 29164349)
J Chem Theory Comput. 2024 Dec 24;20(24):10961-10971. (PMID: 39670846)
Nucleic Acids Res. 2003 Jul 15;31(14):3982-92. (PMID: 12853614)
Front Nutr. 2023 Jan 11;9:1118900. (PMID: 36712498)
ChemMedChem. 2015 Jul;10(7):1141-8. (PMID: 25891095)
Methods Enzymol. 2024;697:151-180. (PMID: 38816122)
Proteins. 2010 Apr;78(5):1084-104. (PMID: 20017216)
iScience. 2022 Dec 30;26(1):105920. (PMID: 36686396)
Pharm Res. 1997 Feb;14(2):164-8. (PMID: 9090703)
Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10260-5. (PMID: 12149447)
Drug Discov Today. 2015 Aug;20(8):969-77. (PMID: 25801181)
Int J Mol Sci. 2024 Feb 01;25(3):. (PMID: 38339078)
Prog Med Chem. 2021;60:273-343. (PMID: 34147204)
Nat Protoc. 2010 Apr;5(4):725-38. (PMID: 20360767)
Trends Pharmacol Sci. 2015 Sep;36(9):579-86. (PMID: 26143240)
Biophys Rev. 2017 Apr;9(2):91-102. (PMID: 28510083)
Antibiotics (Basel). 2022 Jul 13;11(7):. (PMID: 35884190)
Methods Mol Biol. 2017;1561:139-169. (PMID: 28236237)
Chem Rev. 2018 Feb 28;118(4):1691-1741. (PMID: 29319301)
J Chem Phys. 2004 Jun 22;120(24):11919-29. (PMID: 15268227)
Front Endocrinol (Lausanne). 2018 Jun 14;9:329. (PMID: 29963014)
Molecules. 2024 Oct 21;29(20):. (PMID: 39459333)
Biofactors. 2023 Mar;49(2):251-269. (PMID: 36326181)
Chem Biol Drug Des. 2012 Aug;80(2):182-93. (PMID: 22515569)
Pept Sci (Hoboken). 2020 Jan;112(1):. (PMID: 33575525)
Chembiochem. 2013 Mar 18;14(5):617-24. (PMID: 23426877)
Protein Sci. 2020 Jan;29(1):211-222. (PMID: 31682301)
Mol Neurodegener. 2023 Nov 9;18(1):80. (PMID: 37940962)
Int J Mol Sci. 2019 Mar 19;20(6):. (PMID: 30893780)
J Phys Chem Lett. 2016 May 19;7(10):1805-10. (PMID: 27128113)
Bioinformatics. 2019 Oct 15;35(20):4170-4172. (PMID: 30865258)
Drug Discov Today. 2019 Sep;24(9):1821-1835. (PMID: 31229665)
Brief Bioinform. 2021 Nov 5;22(6):. (PMID: 34396417)
Nat Commun. 2022 Jan 10;13(1):176. (PMID: 35013344)
Biophys J. 2005 Aug;89(2):867-75. (PMID: 15908573)
Biochim Biophys Acta Biomembr. 2017 Aug;1859(8):1388-1395. (PMID: 28479275)
J Phys Chem B. 2024 Jun 6;128(22):5281-5292. (PMID: 38785765)
Front Cell Dev Biol. 2020 May 19;8:350. (PMID: 32509780)
QRB Discov. 2022 Sep 19;3:e17. (PMID: 37529282)
Molecules. 2018 Sep 14;23(9):. (PMID: 30223458)
PLoS Comput Biol. 2011 Aug;7(8):e1002131. (PMID: 21876662)
Biophys Chem. 2021 Jun;273:106565. (PMID: 33780688)
Biotechnol Adv. 2011 Nov-Dec;29(6):923-9. (PMID: 21824512)
Curr Opin Struct Biol. 2023 Feb;78:102526. (PMID: 36621153)
Curr Opin Struct Biol. 2014 Apr;25:126-34. (PMID: 24841242)
Signal Transduct Target Ther. 2023 Mar 14;8(1):115. (PMID: 36918529)
J Phys Chem B. 2015 May 28;119(21):6412-20. (PMID: 25941740)
Sci Rep. 2015 Oct 23;5:15568. (PMID: 26492886)
Biomed Pharmacother. 2024 Jun;175:116709. (PMID: 38713945)
J Comput Chem. 2018 Oct 30;39(28):2409-2413. (PMID: 30368849)
J Chem Inf Model. 2025 Feb 24;65(4):2052-2065. (PMID: 39907634)
Front Pharmacol. 2018 Aug 22;9:923. (PMID: 30186166)
Database (Oxford). 2021 Sep 3;2021:. (PMID: 34478499)
Front Med Technol. 2020 Dec 11;2:610997. (PMID: 35047892)
J Chem Theory Comput. 2021 Apr 13;17(4):2630-2639. (PMID: 33779166)
Front Chem. 2020 Apr 28;8:343. (PMID: 32411671)
Ther Deliv. 2025 Jan;16(1):63-86. (PMID: 39411995)
Bioinformatics. 2017 Oct 15;33(20):3299-3301. (PMID: 28430871)
Neuron. 2018 Sep 19;99(6):1129-1143. (PMID: 30236283)
J Chem Theory Comput. 2016 Sep 13;12(9):4524-33. (PMID: 27529120)
Nat Commun. 2024 Feb 21;15(1):1611. (PMID: 38383543)
Mol Cancer Ther. 2009 Oct;8(10):2861-71. (PMID: 19825804)
Methods Mol Biol. 2024;2719:1-11. (PMID: 37803109)
J Pharm Biomed Anal. 2024 Jan 20;238:115836. (PMID: 37939549)
J Comput Chem. 2005 Dec;26(16):1781-802. (PMID: 16222654)
Signal Transduct Target Ther. 2022 Feb 14;7(1):48. (PMID: 35165272)
Proteins. 2003 Sep 1;52(4):609-23. (PMID: 12910460)
Chem Rev. 2021 Feb 24;121(4):2292-2324. (PMID: 33426882)
Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54. (PMID: 27131374)
Int J Mol Sci. 2023 Apr 25;24(9):. (PMID: 37175549)
J Chem Inf Model. 2022 Jun 27;62(12):2999-3007. (PMID: 35699524)
Molecules. 2020 Sep 29;25(19):. (PMID: 33003506)
Mol Ther. 2024 Jun 5;32(6):1687-1700. (PMID: 38582966)
J Phys Chem B. 2013 Jan 17;117(2):518-26. (PMID: 23215032)
Methods Mol Biol. 2022;2405:151-167. (PMID: 35298813)
PLoS One. 2014 May 06;9(5):e94769. (PMID: 24801496)
J Comput Chem. 2015 Jul 30;36(20):1536-49. (PMID: 26096263)
Acc Chem Res. 2021 Sep 21;54(18):3604-3617. (PMID: 34505781)
Acc Chem Res. 2003 Nov;36(11):858-65. (PMID: 14622033)
Peptides. 2005 Feb;26(2):197-206. (PMID: 15629531)
Sci Rep. 2016 Apr 18;6:24439. (PMID: 27087366)
Wiley Interdiscip Rev Comput Mol Sci. 2024 Jan-Feb;14(1):. (PMID: 38680429)
PLoS One. 2024 Apr 23;19(4):e0300688. (PMID: 38652734)
Int J Pharm. 2023 Mar 5;634:122643. (PMID: 36709014)
Proteins. 2004 Nov 1;57(2):225-42. (PMID: 15340911)
Phys Rev Lett. 2007 Apr 6;98(14):146401. (PMID: 17501293)
Int J Mol Sci. 2019 Nov 27;20(23):. (PMID: 31783634)
Chem Rev. 2014 Jan 22;114(2):901-26. (PMID: 24446748)
Heliyon. 2024 Jan 11;10(2):e24515. (PMID: 38293362)
Biophys Chem. 2017 Apr;223:11-16. (PMID: 28187350)
BMC Struct Biol. 2012 Aug 02;12:18. (PMID: 22857400)
J Comput Aided Mol Des. 2020 Dec;34(12):1261-1273. (PMID: 33009624)
Bioinformatics. 2019 Dec 15;35(24):5121-5127. (PMID: 31161213)
Chembiochem. 2024 Feb 1;25(3):e202300481. (PMID: 38009768)
J Chem Phys. 2017 Oct 21;147(15):152725. (PMID: 29055328)
J Biomol Struct Dyn. 2019 Feb;37(3):726-740. (PMID: 29421954)
J Pept Sci. 2008 Mar;14(3):283-9. (PMID: 17918765)
Food Chem. 2023 Mar 30;405(Pt A):134737. (PMID: 36335734)
J Phys Chem B. 2010 Mar 4;114(8):2549-64. (PMID: 20136072)
Protein Sci. 2017 Nov;26(11):2195-2206. (PMID: 28815769)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
J Phys Chem Lett. 2015 Jun 4;6(11):2127-33. (PMID: 26266514)
Biochim Biophys Acta. 2008 Jul-Aug;1778(7-8):1528-36. (PMID: 18358231)
Biochem Biophys Res Commun. 1993 Dec 15;197(2):360-5. (PMID: 7903526)
J Chem Inf Model. 2022 Jul 11;62(13):3142-3156. (PMID: 35727311)
Nutrients. 2022 Nov 14;14(22):. (PMID: 36432497)
Brief Bioinform. 2024 May 23;25(4):. (PMID: 38856172)
Biophys J. 2023 Jul 25;122(14):2833-2840. (PMID: 36738105)
J Med Chem. 2016 May 12;59(9):4035-61. (PMID: 26807648)
Proteins. 2011;79 Suppl 10:74-90. (PMID: 22069034)
Chem Rev. 2019 Sep 11;119(17):10241-10287. (PMID: 31083977)
Curr Opin Struct Biol. 2013 Dec;23(6):894-902. (PMID: 24138780)
Bioinformatics. 2019 Feb 15;35(4):694-695. (PMID: 30101282)
Molecules. 2018 Aug 20;23(8):. (PMID: 30127265)
Acc Chem Res. 2017 Aug 15;50(8):1847-1854. (PMID: 28715199)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
Sci Rep. 2020 Feb 10;10(1):2194. (PMID: 32042035)
Molecules. 2021 Oct 27;26(21):. (PMID: 34770898)
J Comput Chem. 2009 Jul 30;30(10):1545-614. (PMID: 19444816)
Comput Struct Biotechnol J. 2022 Dec 19;21:463-471. (PMID: 36618982)
J Chem Inf Model. 2023 Dec 25;63(24):7791-7806. (PMID: 37955428)
Adv Biosyst. 2018 May;2(5):. (PMID: 30800727)
Essays Biochem. 2020 Oct 8;64(4):649-680. (PMID: 32975287)
Adv Protein Chem. 2003;66:27-85. (PMID: 14631816)
Int J Mol Sci. 2020 Sep 01;21(17):. (PMID: 32882859)
Biomacromolecules. 2015 Aug 10;16(8):2347-55. (PMID: 26156023)
Science. 2011 Oct 28;334(6055):517-20. (PMID: 22034434)
Brief Bioinform. 2024 Mar 27;25(3):. (PMID: 38678388)
J Food Sci Technol. 2019 Feb;56(2):535-547. (PMID: 30906011)
Micron. 2002;33(4):365-84. (PMID: 11814876)
Nat Struct Biol. 2002 Sep;9(9):646-52. (PMID: 12198485)
Nat Methods. 2007 Oct;4(10):807-15. (PMID: 17901870)
J Chem Inf Model. 2018 Aug 27;58(8):1473-1482. (PMID: 29975531)
Brief Bioinform. 2024 Mar 27;25(3):. (PMID: 38706323)
Phys Chem Chem Phys. 2021 Jan 6;23(1):607-616. (PMID: 33331371)
Biophys J. 1999 May;76(5):2448-59. (PMID: 10233062)
Brief Bioinform. 2017 Sep 1;18(5):870-885. (PMID: 27402792)
Protein Sci. 2002 Jul;11(7):1729-37. (PMID: 12070326)
Pharmaceuticals (Basel). 2021 Apr 06;14(4):. (PMID: 33917313)
ACS Bio Med Chem Au. 2022 Dec 21;3(1):1-31. (PMID: 37101606)
Drugs. 2017 Apr;77(5):593-598. (PMID: 28255961)
IUBMB Life. 2009 Jun;61(6):627-43. (PMID: 19472192)
J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576)
Patterns (N Y). 2020 Nov 12;1(9):100142. (PMID: 33336200)
J Dairy Sci. 2024 May;107(5):2633-2652. (PMID: 38101739)
Biochim Biophys Acta. 2015 May;1850(5):872-877. (PMID: 25450171)
Int J Mol Sci. 2024 Jan 23;25(3):. (PMID: 38338676)
Methods Mol Biol. 2010;673:73-94. (PMID: 20835794)
Front Bioinform. 2022 Oct 21;2:1046493. (PMID: 36338806)
Proteins. 2013 Dec;81(12):2119-28. (PMID: 23913867)
Curr Opin Struct Biol. 2017 Apr;43:88-94. (PMID: 27984811)
Methods Mol Biol. 2019;2022:179-200. (PMID: 31396904)
Beilstein J Org Chem. 2016 Dec 12;12:2694-2718. (PMID: 28144341)
Front Microbiol. 2020 Nov 12;11:563030. (PMID: 33281761)
Int J Mol Sci. 2015 Jul 28;16(8):17193-230. (PMID: 26225966)
Med Res Rev. 2024 May;44(3):1147-1182. (PMID: 38173298)
Food Funct. 2019 Sep 1;10(9):6030-6041. (PMID: 31483433)
J Pharm Sci. 2009 Apr;98(4):1223-45. (PMID: 18661536)
Pharmaceuticals (Basel). 2020 Dec 03;13(12):. (PMID: 33287352)
PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. (PMID: 28746339)
ACS Infect Dis. 2024 Feb 9;10(2):763-778. (PMID: 38259029)
Physiol Rev. 2007 Oct;87(4):1409-39. (PMID: 17928588)
PLoS One. 2012;7(10):e46688. (PMID: 23056405)
Acc Chem Res. 2021 Sep 21;54(18):3576-3592. (PMID: 34406761)
J Chem Inf Model. 2024 May 27;64(10):4310-4321. (PMID: 38739853)
Structure. 2010 Feb 10;18(2):188-99. (PMID: 20159464)
Protein Eng Des Sel. 2022 Feb 17;35:. (PMID: 35174855)
Biochemistry. 1966 Jan;5(1):365-85. (PMID: 5938952)
RSC Adv. 2019 Oct 30;9(60):35089-35097. (PMID: 35530686)
J Am Soc Nephrol. 2013 Jul;24(8):1250-61. (PMID: 23813215)
Nat Rev Drug Discov. 2020 Jun;19(6):389-413. (PMID: 32494050)
Brief Bioinform. 2015 Nov;16(6):1045-56. (PMID: 25900849)
Proteins. 2017 Mar;85(3):378-390. (PMID: 27701780)
Eur J Med Chem. 2022 Dec 5;243:114766. (PMID: 36122548)
Drugs. 2020 Feb;80(2):197-208. (PMID: 32002850)
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6732-7. (PMID: 15814618)
J Med Chem. 2017 Nov 9;60(21):8982-8988. (PMID: 29028171)
Biomol Ther (Seoul). 2012 Jan;20(1):19-26. (PMID: 24116270)
Curr Comput Aided Drug Des. 2011 Jun;7(2):146-57. (PMID: 21534921)
Molecules. 2017 Nov 22;22(11):. (PMID: 29165360)
Structure. 2024 Feb 1;32(2):228-241.e4. (PMID: 38113889)
Database (Oxford). 2018 Jan 1;2018:. (PMID: 29688386)
Front Mol Biosci. 2021 Apr 28;8:669431. (PMID: 33996914)
Bioorg Med Chem. 2018 Mar 15;26(6):1135-1150. (PMID: 29295762)
Annu Rev Biophys. 2019 May 6;48:371-394. (PMID: 30916997)
J Med Chem. 1997 Nov 21;40(24):3979-85. (PMID: 9397180)
Mol Aspects Med. 2013 Apr-Jun;34(2-3):323-36. (PMID: 23506874)
J Chem Theory Comput. 2020 Jun 9;16(6):3959-3969. (PMID: 32324992)
Brief Bioinform. 2023 Nov 22;25(1):. (PMID: 38233090)
Angew Chem Int Ed Engl. 2024 Jan 15;63(3):e202308251. (PMID: 37870189)
BMC Cancer. 2023 Jul 26;23(1):699. (PMID: 37495988)
N Engl J Med. 1996 Jan 25;334(4):246-54. (PMID: 8532003)
J R Soc Interface. 2012 Jan 7;9(66):20-33. (PMID: 21993006)
Molecules. 2018 Jul 30;23(8):. (PMID: 30061498)
J Chem Theory Comput. 2010 Nov 9;6(11):3569-79. (PMID: 26617103)
Transl Neurodegener. 2017 Mar 13;6:6. (PMID: 28293421)
PLoS One. 2013;8(3):e58769. (PMID: 23516555)
Ann Pharmacother. 2014 Nov;48(11):1494-501. (PMID: 25136065)
Sci Rep. 2024 May 25;14(1):11995. (PMID: 38796582)
Sci Signal. 2012 Sep 25;5(243):pe40. (PMID: 23012652)
JACS Au. 2021 Aug 04;1(9):1330-1341. (PMID: 34604842)
Int J Mol Sci. 2024 Sep 21;25(18):. (PMID: 39337622)
Pharmaceuticals (Basel). 2022 Oct 19;15(10):. (PMID: 36297395)
Molecules. 2019 Apr 30;24(9):. (PMID: 31052253)
Curr Opin Struct Biol. 2020 Apr;61:160-166. (PMID: 32006812)
Protein Sci. 2023 Oct;32(10):e4778. (PMID: 37695921)
BMC Bioinformatics. 2007 Aug 01;8:280. (PMID: 17678535)
Expert Rev Anti Infect Ther. 2005 Apr;3(2):191-9. (PMID: 15918777)
Digit Discov. 2022 Mar 31;1(3):195-208. (PMID: 35769205)
J Phys Chem B. 2022 Sep 15;126(36):6922-6935. (PMID: 36067064)
Nat Rev Drug Discov. 2020 Apr;19(4):277-289. (PMID: 31848464)
Clin Transl Med. 2022 Aug;12(8):e1011. (PMID: 35968909)
Methods Mol Biol. 2012;857:375-98. (PMID: 22323231)
Curr Pharm Biotechnol. 2022;23(13):1541-1555. (PMID: 34994325)
N Engl J Med. 2014 Jul 17;371(3):224-33. (PMID: 25014687)
Curr Comput Aided Drug Des. 2011 Mar;7(1):10-22. (PMID: 20807187)
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):426. (PMID: 30717654)
Nat Commun. 2018 Sep 24;9(1):3887. (PMID: 30250077)
Comput Struct Biotechnol J. 2020 Jun 30;18:1774-1789. (PMID: 32695270)
ACM Trans Reconfigurable Technol Syst. 2010 Nov;3(4):. (PMID: 21660208)
Nucleic Acids Res. 2016 Jul 8;44(W1):W522-8. (PMID: 27131789)
Food Funct. 2022 Dec 13;13(24):12510-12540. (PMID: 36420754)
J Chem Theory Comput. 2017 Mar 14;13(3):1034-1043. (PMID: 28245118)
Curr Res Food Sci. 2023 Sep 17;7:100592. (PMID: 37766891)
Methods. 2020 Aug 1;180:89-110. (PMID: 32645448)
J Chem Theory Comput. 2021 Oct 12;17(10):6634-6646. (PMID: 34524800)
Annu Rev Biochem. 2024 Aug;93(1):389-410. (PMID: 38594926)
Curr Opin Struct Biol. 2008 Apr;18(2):140-8. (PMID: 18304802)
J Chem Theory Comput. 2022 Oct 11;18(10):6324-6333. (PMID: 36190318)
Methods Mol Biol. 2015;1268:241-71. (PMID: 25555728)
Int J Mol Sci. 2021 Feb 05;22(4):. (PMID: 33562633)
Proteins. 2017 Mar;85(3):359-377. (PMID: 27865038)
Amino Acids. 2024 May 31;56(1):37. (PMID: 38822212)
Br J Cancer. 2001 Nov;85 Suppl 2:1-5. (PMID: 11900209)
Nat Microbiol. 2022 Oct;7(10):1661-1672. (PMID: 36163500)
Nat Neurosci. 2018 Oct;21(10):1332-1340. (PMID: 30250260)
Methods Mol Biol. 2012;819:59-74. (PMID: 22183530)
Proteins. 2013 Dec;81(12):2096-105. (PMID: 24123488)
J Comput Aided Mol Des. 2012 Jun;26(6):775-86. (PMID: 22566074)
Biochim Biophys Acta. 2013 Nov;1828(11):2524-31. (PMID: 23756777)
Arch Biochem Biophys. 2008 Jan 1;469(1):100-17. (PMID: 17588526)
J Chem Theory Comput. 2023 Jul 25;19(14):4338-4350. (PMID: 37358079)
Membranes (Basel). 2022 Sep 16;12(9):. (PMID: 36135911)
Sci Rep. 2016 Dec 01;6:37532. (PMID: 27905468)
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273. (PMID: 23341755)
Curr Med Chem. 2013;20(15):1985-96. (PMID: 23317161)
Curr Protein Pept Sci. 2006 Jun;7(3):217-27. (PMID: 16787261)
J Phys Chem Lett. 2014 Sep 18;5(18):3144-3150. (PMID: 25247054)
J Med Chem. 2015 Sep 24;58(18):7370-80. (PMID: 26308095)
Sci Rep. 2023 Aug 17;13(1):13398. (PMID: 37592012)
PLoS Comput Biol. 2020 Apr 2;16(4):e1007449. (PMID: 32240155)
Nat Protoc. 2017 Feb;12(2):255-278. (PMID: 28079879)
Structure. 2010 Oct 13;18(10):1233-43. (PMID: 20947012)
Methods Mol Biol. 2015;1266:29-53. (PMID: 25560066)
Int J Biol Macromol. 2022 Dec 31;223(Pt A):143-160. (PMID: 36356861)
Genes (Basel). 2023 May 29;14(6):. (PMID: 37372372)
J Chem Inf Model. 2024 Mar 25;64(6):2112-2124. (PMID: 38483249)
Nat Commun. 2021 Jun 18;12(1):3584. (PMID: 34145237)
Cells. 2022 Dec 12;11(24):. (PMID: 36552778)
Cureus. 2024 Jul 2;16(7):e63646. (PMID: 39092344)
P T. 2010 Sep;35(9):498-529. (PMID: 20975808)
Curr Opin Struct Biol. 2024 Aug;87:102829. (PMID: 38848655)
Nucleic Acids Res. 2015 Jul 1;43(W1):W431-5. (PMID: 25969449)
Protein Sci. 2004 Nov;13(11):2909-24. (PMID: 15498937)
Methods Mol Biol. 2015;1215:151-71. (PMID: 25330963)
Int J Mol Sci. 2014 Feb 14;15(2):2622-45. (PMID: 24534807)
Bioinformatics. 2013 Jul 01;29(13):1698-9. (PMID: 23661696)
Chem Rev. 2022 Sep 28;122(18):14085-14179. (PMID: 35921495)
Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1635-51. (PMID: 26766517)
Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9438-41. (PMID: 22645367)
PLoS One. 2016 Nov 15;11(11):e0166460. (PMID: 27846259)
Sci Rep. 2022 Jan 19;12(1):984. (PMID: 35046419)
Nat Protoc. 2021 Dec;16(12):5634-5651. (PMID: 34759384)
Nutr Res. 2017 Oct;46:22-30. (PMID: 29173648)
Angew Chem Int Ed Engl. 2023 Feb 6;62(7):e202213362. (PMID: 36542066)
J Agric Food Chem. 2003 Jun 4;51(12):3668-74. (PMID: 12769543)
Bioanalysis. 2023 Nov;15(21):1315-1325. (PMID: 37737150)
Front Bioinform. 2022 Sep 26;2:959160. (PMID: 36304330)
Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658)
Proteins. 2016 Oct;84(10):1390-407. (PMID: 27287023)
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W249-53. (PMID: 21622962)
RSC Adv. 2023 Dec 11;13(51):35947-35963. (PMID: 38090079)
Expert Rev Proteomics. 2021 Jul;18(7):527-556. (PMID: 34343059)
PNAS Nexus. 2024 Nov 27;3(12):pgae541. (PMID: 39660074)
Nucleic Acids Res. 2018 Jul 2;46(W1):W443-W450. (PMID: 29746661)
Drug Discov Today. 2006 Jul;11(13-14):580-94. (PMID: 16793526)
PLoS Comput Biol. 2009 Aug;5(8):e1000475. (PMID: 19696878)
Food Res Int. 2015 Oct;76(Pt 3):518-526. (PMID: 28455033)
Nucleic Acids Res. 2017 Jul 3;45(W1):W361-W364. (PMID: 28460116)
J Chem Inf Model. 2023 Feb 13;63(3):835-845. (PMID: 36724090)
Comput Struct Biotechnol J. 2019 Jul 26;17:1162-1170. (PMID: 31462972)
J Phys Chem B. 2006 Mar 16;110(10):5025-44. (PMID: 16526746)
PLoS Comput Biol. 2017 Dec 27;13(12):e1005905. (PMID: 29281622)
J Am Chem Soc. 2003 Feb 19;125(7):1731-7. (PMID: 12580598)
Drug Discov Today. 2018 Aug;23(8):1530-1537. (PMID: 29733895)
Pharmaceuticals (Basel). 2023 Jul 12;16(7):. (PMID: 37513908)
Proteins. 2010 Jun;78(8):1950-8. (PMID: 20408171)
Infect Immun. 2021 Mar 17;89(4):. (PMID: 33558318)
Molecules. 2017 Nov 08;22(11):. (PMID: 29117144)
Biochim Biophys Acta. 2006 Oct;1758(10):1596-608. (PMID: 16956577)
Biochem Pharmacol. 1999 Dec 1;58(11):1775-80. (PMID: 10571252)
Angew Chem Int Ed Engl. 2025 Mar 03;64(10):e202414325. (PMID: 39611429)
Drug Discov Today. 2014 Jul;19(7):890-7. (PMID: 24216321)
J Chem Theory Comput. 2022 Oct 11;18(10):6386-6395. (PMID: 36149394)
Proteins. 2020 Aug;88(8):1037-1049. (PMID: 31891416)

847402 Supported by Enterprise Ireland and received funding from the European Union Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie

Keywords: AlphaFold; Protein Language Models; bioactive peptides; homology modelling; molecular docking; molecular dynamics simulation; molecular modelling; virtual screening

0 (Peptides)

Date Created: 20250430 Date Completed: 20250430 Latest Revision: 20250514

20250514

PMC12025251

10.3390/biom15040524

40305228