通过在文本化蛋白质-连接物相互作用上训练的大型语言模型系统地探索小分子结合
Taeseob Lee1,2, Heehoon Jung1, Ahnjae Jung1,3
1Syntekabio Inc., 18 Gukjegwahak 17-ro, Yuseong-gu, Daejeon 34002, Republic of Korea.
Molecules (Basel, Switzerland)
|December 11, 2025
概括
大型语言模型 (LLM) 现在可以通过将3D分子结构转换为语言来分析生物物理数据. 这种方法揭示了新的药物相互作用和蛋白质网络,推动了药物发现.
科学领域:
- 计算化学是一种计算化学.
- 生物物理学的生物物理.
- 人工智能的人工智能是人工智能.
背景情况:
- 大型语言模型 (LLM) 展示了广泛的任务性能.
- 为生物物理应用利用LLM需要将3D化学数据转换为类似于1D语言的格式.
- 一个关键的挑战是有效地转换和标记化分子数据用于LLM处理.
研究的目的:
- 开发一种方法来将分子数据转化为类似语言的表示,以便在生物物理学中利用LLM.
- 训练和验证模型使用已知的蛋白质 - 连接体复合体.
- 为了使LLMs能够评估化学性质,识别结合相似性,并发现相关药物.
主要方法:
- 开发一种新的方法,将3D分子数据转换为1D语言类序列.
- 为LLM输入生成的语言类数据的标记化.
- 训练和验证模型在蛋白质 - 配体复杂数据集上的模型.
- 使用预训练模型分析化学性质,结合相互作用和药物关系.
主要成果:
- 该模型成功地将分子数据转换为LLMs的可处理语言格式.
- 使用蛋白质 - 配体复合物的验证证实了该模型评估化学性质和结合特性的能力.
- 该模型确定了共享的结合性质和结构,并揭示了相关的药物.
- 开发的语言和模型揭示了以前未报告的蛋白质-蛋白质网络,受连接体相互作用的影响.
结论:
- 该研究提出了一种可行的方法,通过创建一个分子语言,将LLMs应用于生物物理数据.
- 该模型通过识别新型相互作用和相关化合物来证明药物发现的潜力.
- 这种方法为了解复杂的生物网络和联体介导效应开辟了新的途径.
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