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ColabDesign and AlphaFold Running Locally: AI Protein Structure Modeling for Drug Design
Source: https://www.exxactcorp.com/blog/molecular-dynamics/colabdesign-design-novel-proteins-with-targeted-structure Advances in deep learning for protein structures have accelerated at a remarkable pace in the last few years. This has opened up a window into the myriad roles of proteins in biology and medicine and their potential to engineer-to-order capabilities displayed by proteins in nature, and more. The most obvious application for deep…
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Full-Atom Peptide Design based on Multi-modal Flow Matching
License: CC BY 4.0 arXiv:2406.00735v1 [q-bio.BM] 02 Jun 2024 Jiahan LiChaoran ChengZuofan WuRuihan GuoShitong LuoZhizhou RenJian PengJianzhu Ma Abstract Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first multi-modal deep…
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Cyclopeptide Ligand Generation
Cyclopeptides, with their diverse building blocks and intricate three-dimensional architectures, offer unique opportunities for targeting some of the most challenging biological interactions, such as protein-peptide interactions. As nature has not evolved a specific ligand for every conceivable target, leveraging both traditional and computational methodologies has become crucial in generating novel cyclopeptide ligands for various proteins.…
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Cyclopeptide Chemical Synthesis
Since Emil Fischer pioneered peptide synthesis in 1901, the techniques for synthesizing peptides have significantly advanced. Innovations such as solid-phase peptide synthesis (SPPS), various protection and deprotection strategies, efficient coupling agents, automation, and high-yielding cyclization methods have all contributed to today’s ability to produce peptides. The modular nature of peptides and the effective coupling of…
