Daly NL, Craik DJ (2009) Structural studies of conotoxins. IUBMB Life 61:144–150
Article CAS PubMed Google Scholar
Lewis RJ, Dutertre S, Vetter I, Christie MJ (2012) Conus venom peptide pharmacology. Pharmacol Rev 64:259–298
Article CAS PubMed Google Scholar
Pope JE, Deer TR (2013) Ziconotide: a clinical update and pharmacologic review. Expert Opin Pharmacother 14:957–966
Article CAS PubMed Google Scholar
Gao B, Peng C, Yang J, Yi Y, Zhang J, Shi Q (2017) Cone snails: a big store of Conotoxins for Novel Drug Discovery. Toxins (Basel) 9
Li X, Liu H, Gao C, Li Y, Jia D, Yang Y, Yang J, Wei Z, Jiang T, Yu R (2020) ConoMode, a database for conopeptide binding modes. Database (Oxford) 2020
Gao B, Huang Y, Peng C, Lin B, Liao Y, Bian C, Yang J, Shi Q (2022) High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development. Biodes Res 2022:9895270
Lewis RJ, Garcia ML (2003) Therapeutic potential of venom peptides. Nat Rev Drug Discov 2:790–802
Article CAS PubMed Google Scholar
Fu Y, Li C, Dong S, Wu Y, Zhangsun D, Luo S (2018) Discovery Methodology of Novel conotoxins from Conus Species. Mar Drugs 16
Fu Y, Zhang Y, Ju S, Ma B, Huang W, Luo S (2022) Isolation and characterization of five novel disulfide-poor conopeptides from Conus marmoreus venom. J Venom Anim Toxins Incl Trop Dis 28:e20210116
Article CAS PubMed PubMed Central Google Scholar
Craik DJ, Adams DJ (2007) Chemical modification of conotoxins to improve stability and activity. ACS Chem Biol 2:457–468
Article CAS PubMed Google Scholar
Wu X, Hone AJ, Huang YH, Clark RJ, McIntosh JM, Kaas Q, Craik DJ (2023) Computational Design of alpha-Conotoxins to Target Specific Nicotinic Acetylcholine Receptor Subtypes. Chemistry:e202302909
Naraga AMB, Belleza OJV, Villaraza AJL (2018) Total synthesis of mu-conotoxin lt5d. RSC Adv 8:36579–36583
Article CAS PubMed PubMed Central Google Scholar
Souf YM, Lokaj G, Kuruva V, Saed Y, Raviglione D, Brik A, Nicke A, Inguimbert N, Dutertre S (2023) Synthesis and Biological Activity of Novel alpha-Conotoxins Derived from Endemic Polynesian Cone Snails. Mar Drugs 21
Repecka D, Jauniskis V, Karpus L, Rembeza E, Rokaitis I, Zrimec J, Poviloniene S, Laurynenas A, Viknander S, Abuajwa W, Savolainen O, Meskys R, Engqvist MKM, Zelezniak A (2021) Expanding functional protein sequence spaces using generative adversarial networks. Nat Mach Intell 3:324–333
Madani A, Krause B, Greene ER, Subramanian S, Mohr BP, Holton JM, Olmos JL Jr., Xiong C, Sun ZZ, Socher R, Fraser JS, Naik N (2023) Large language models generate functional protein sequences across diverse families. Nat Biotechnol 41:1099–1106
Article CAS PubMed PubMed Central Google Scholar
Ferruz N, Schmidt S, Hocker B (2022) ProtGPT2 is a deep unsupervised language model for protein design. Nat Commun 13:4348
Article CAS PubMed PubMed Central Google Scholar
Xu B, Chen Y, Xue W (2023) Computational protein design - where it goes? Curr Med Chem
Dauparas J, Anishchenko I, Bennett N, Bai H, Ragotte RJ, Milles LF, Wicky BIM, Courbet A, de Haas RJ, Bethel N, Leung PJY, Huddy TF, Pellock S, Tischer D, Chan F, Koepnick B, Nguyen H, Kang A, Sankaran B, Bera AK, King NP, Baker D (2022) Robust deep learning-based protein sequence design using ProteinMPNN. Science 378:49–56
Article CAS PubMed PubMed Central Google Scholar
Das P, Sercu T, Wadhawan K, Padhi I, Gehrmann S, Cipcigan F, Chenthamarakshan V, Strobelt H, Dos SC, Chen PY, Yang YY, Tan JPK, Hedrick J, Crain J, Mojsilovic A (2021) Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations. Nat Biomed Eng 5:613–623
Article CAS PubMed Google Scholar
Yang L, Yang G, Bing Z, Tian Y, Huang L, Niu Y, Yang L (2022) Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm. Brief Bioinform 23.
Kaas Q, Yu R, Jin AH, Dutertre S, Craik DJ (2012) ConoServer: updated content, knowledge, and discovery tools in the conopeptide database. Nucleic Acids Res 40:D325–D330
Article CAS PubMed Google Scholar
Li Y, Li F, Duan Z, Liu R, Jiao W, Wu H, Zhu F, Xue W (2024) SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae893
Article PubMed PubMed Central Google Scholar
Wang X, Zhang Y, Li Z, Duan Z, Guo M, Wang Z, Zhu F, Xue W (2024) PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering. Nucleic Acids Res 52:W272–W279. https://doi.org/10.1093/nar/gkae384
Article PubMed PubMed Central Google Scholar
Akondi KB, Muttenthaler M, Dutertre S, Kaas Q, Craik DJ, Lewis RJ, Alewood PF (2014) Discovery, synthesis, and structure-activity relationships of conotoxins. Chem Rev 114:5815–5847
Article CAS PubMed PubMed Central Google Scholar
F Z ZQ, H X and Q H (2021) K D, D X, Y Z, H Z, A Comprehensive Survey on Transfer Learning. Proceedings of the IEEE 109:43–76
Bengio Y, Ducharme R, Vincent P, Jauvin C (2003) A neural probabilistic language model. J Mach Learn Res 3:1137–1155
Madani A, McCann B, Naik N, Keskar N, Anand N, Eguchi R, Huang P, Socher R (2020) ProGen: Language Modeling for Protein Generation
Hu X, Chu L, Pei J, Liu W, Bian J (2021) Model complexity of deep learning: a survey. Knowl Inf Syst 63:2585–2619
Nikolados E-M, Wongprommoon A, Aodha OM, Cambray G, Oyarzún (2022) DA Accuracy and data efficiency in deep learning models of protein expression. Nature Communications 13:7755
Sutskever I, Vinyals O, Le QV (2014) Sequence to sequence learning with neural networks. Proceedings of the 27th International Conference on Neural Information Processing Systems - Volume 2, MIT Press, Montreal, Canada pp. 3104–3112
Bhopatkar AA, Uversky VN, Rangachari V (2020) Disorder and cysteines in proteins: a design for orchestration of conformational see-saw and modulatory functions. Prog Mol Biol Transl Sci 174:331–373
Article CAS PubMed PubMed Central Google Scholar
Kaas Q, Westermann JC, Halai R, Wang CK, Craik DJ (2008) ConoServer, a database for conopeptide sequences and structures. Bioinformatics 24:445–446
Article CAS PubMed Google Scholar
Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S (2019) Snails in Silico: a review of computational studies on the conopeptides. Mar Drugs 17
(2023) UniProt: the Universal protein knowledgebase in 2023. Nucleic Acids Res 51:D523–D531
Xie Z, Sato I, Sugiyama M (2020) On the overlooked pitfalls of Weight Decay and how to mitigate them. A Gradient-Norm Perspective
Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M (2022) ColabFold: making protein folding accessible to all. Nat Methods 19:679–682
Article CAS PubMed PubMed Central Google Scholar
Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the Accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713
Comments (0)