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Nature Biotechnology:西湖大学原发杰/常兴团队等开发ProTrek,以自然语言“导航”蛋白质宇宙
生物世界· 2025-10-03 01:00
Core Insights - The article discusses the development of ProTrek, a novel trimodal protein language model that integrates amino acid sequences, three-dimensional structures, and natural language descriptions for advanced protein searches [3][9][20]. Group 1: Challenges and Opportunities in Protein Research - Proteins are essential for life, and understanding the complex relationship between their sequences, structures, and functions is crucial for molecular science and pharmacology [6]. - Traditional tools like BLAST and Foldseek are limited to single-modal comparisons, hindering the discovery of cross-modal relationships between sequences, structures, and functions [6][9]. - Approximately 30% of proteins in the UniProt database remain functionally unannotated due to their distant phylogenetic relationships with known homologs, likened to "dark matter" in the protein universe [6][9]. Group 2: ProTrek's Innovative Framework - ProTrek employs a unique trimodal framework that unifies three core protein information types: amino acid sequences (1D), three-dimensional structures (spatial), and natural language function descriptions (semantic) [9][20]. - The model utilizes a bidirectional alignment framework to establish strong correlations across sequence-structure, structure-function, and function-sequence dimensions [9][21]. Group 3: Performance and Experimental Validation - ProTrek demonstrates superior performance, outperforming existing top methods like ProteinDT and ProtST by over 30-60 times in standard protein function retrieval benchmarks [11][21]. - The model's global representation learning capability allows it to identify convergent evolution proteins that have significant sequence and structure differences but perform similar functions [11][21]. - Experimental validation showed ProTrek's ability to discover new proteins with similar functions to human UDG, achieving higher editing efficiency and lower off-target effects compared to existing tools [15][23]. Group 4: Implications and Future Prospects - ProTrek enhances the efficiency and depth of protein research, facilitating large-scale annotation of unknown protein functions and accelerating enzyme discovery and drug design [18][23]. - The model's integration of complex molecular data with intuitive natural language promotes a better understanding of the protein world [18][23]. - ProTrek's capabilities are expected to lead to new scientific discoveries across various fields of protein science [18][23].
X @IcoBeast.eth🦇🔊
IcoBeast.eth🦇🔊· 2025-08-14 14:11
DeFi Investment Performance - Initial investment in BLAST tokens was approximately $21 thousand and 53 thousand USDB [1] - USDB holdings increased to $75 thousand, while BLAST tokens are valued at $22 thousand [1] - The investment strategy has covered the initial downside exposure risk on the Blast token [1] - Earning approximately 77% APY on $75 thousand [1] Passive Income Generation - Generating approximately $37 per day from Polkadot farms on Hydration using tBTC and SOL [1] - Crossed the $200 per day mark in passive DeFi income [1] Market Outlook - DeFi is considered the future of wealth creation [1] - The industry believes everyone will eventually participate in DeFi [1]
X @IcoBeast.eth🦇🔊
IcoBeast.eth🦇🔊· 2025-07-21 03:07
DeFi Yield Farming Performance - DeFi yields are presented as a potentially superior method for achieving consistent compounding gains [1] - The author reports earning approximately $160 per day on a capital base of around $120 thousand across various protocols [1] - This translates to an estimated 48% APY, or roughly $5 thousand per month [2] Protocol and Platform Analysis - Blast is highlighted as a top-performing DeFi farm over the past 4 months [1] - The report suggests that yield farming can be effective in diverse market conditions [1] - The author emphasizes the importance of risk management, particularly regarding contract and platform exploits [2] - Solid, battle-tested, or well-respected protocols offering significant incentives are recommended for capital growth [2] Future Outlook and Token Valuation - The author expresses a bullish outlook on Blast, anticipating a price target of $1 per BLAST token [3] - Specific farming strategies include BLAST emission farming, delta neutral funding farming on Liminal, and DOT/gigaDOT farming on Hydration [3]
X @IcoBeast.eth🦇🔊
IcoBeast.eth🦇🔊· 2025-07-18 00:24
DeFi Farming Performance - Hydration 上的 tBTC 堆栈获得约 18% 的年化收益率 (APY),表明 Polkadot DeFi 仍有未被充分利用的潜力 [1] - 通过 HYPE delta neutral funding fees 获得约 9.4% 的年化收益率 (APY),高于闲置在钱包中的收益 [2] - 在 BLAST 上通过稳定币堆栈获得约 75% 的年化收益率 (APY),尽管存在争议,但价格上涨抵消了资本损失 [2] Investment Strategy - 考虑扩大 HYPE 的持有量,并分散到各种现货 Unit 资产中,以防空投 [2] - 正在进行的投票可能会进一步增加 Hydration 池的排放 [1] Market Observation - Polkadot DeFi 似乎仍未得到充分利用 [1]