# MindSpore SPONGE ## 介绍 从精准药物设计、蛋白质结构预测到个性化医疗，AI正在重塑生命科学的研究范式，极大地加速了科学发现的过程。然而，这一融合也对底层计算工具提出了更高要求：传统的模拟软件难以满足AI模型训练与大规模生物数据处理的效率需求。 MindSpore SPONGE(Simulation Package tOwards Next GEneration molecular modelling)是基于昇思MindSpore的AI计算生物领域套件，包含蛋白质结构、序列及功能预测、基因组结构及语言模型等通用模型应用，旨在于为广大的科研人员、老师及学生提供高效、易用的AI计算生物软件。 ## 重要消息 - 🙌`[置顶]` `[进行中]` [**2025 MindScience开源实习任务**](https://atomgit.com/mindspore/community/issues/2027)火热进行中！持续发布新任务，欢迎大家认领~！！[[活动详情]](https://mp.weixin.qq.com/s/R-t8-u4ak2fN4gxe13m3Gw) - 🔥`2025.12.23` 基于MindSpore的Protenix推理及训练发布，支持2K序列！[[代码]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/protenix) - 🔥`2025.11.6` 基于MindSpore的RFdiffusion推理发布，支持抗体设计，性能持续提升中！[[代码]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/rf_diffusion) - 🔥`2025.09.15` 昌平实验室、北京大学高毅勤、刘思睿团队发表基于MindSpore训练的[**GRASP**](https://www.nature.com/articles/s41592-025-02820-1)模型收录《Nature Methods》。该模型整合多源实验信息实现复合物建模，抗体预测超越 AlphaFold3。[[相关新闻]](https://mp.weixin.qq.com/s/OyqGvoIbtZaOTgEM5UFXJw) - 🔥`2025.8.18—2025.8.22` MindSpore SPONGE[**暑期学校第五季**](https://mp.weixin.qq.com/s/GAPyziaXcZyGPSB09BeMgg)圆满收官！[[活动回放]](https://mp.weixin.qq.com/s/loUBlJhIWYAn646w3n3wVA) - 🔥`2025.7.26` 基于MindSpore的DeepMind版AlphaFold3推理发布，性能持续提升中！[[代码]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/AlphaFold3) - 🔥`2025.05.20` 基于MindSpore训练的8亿参数单细胞基础大模型[**CellFM**](https://www.nature.com/articles/s41467-025-59926-5)重磅发布于《Nature Communications》。由中山大学杨跃东研究团队牵头，联合重庆大学曾远松团队，首次实现 1 亿级人类细胞数据高效建模，零样本细胞类型注释等任务性能全面领先。[[相关新闻]](https://mp.weixin.qq.com/s/KW-j92yUfeiS4EFfjZSfLw) - `2023.12.07` 抗体设计天工大模型荣获“2023 AIIA人工智能十大先锋应用案例”, [[相关新闻]](https://mp.weixin.qq.com/s/UQStKzm0fdXbA4RQgLE8fw) - `2023.11.10` MSA生成增强模型MEGA-EvoGen论文"Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction"发表于计算化学期刊JCTC。[[论文]](https://pubs.acs.org/doi/10.1021/acs.jctc.3c00528?cookieSet=1) [[代码]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/MEGAProtein.md) - `2023.6.26` MindSPONGE论文"Artificial Intelligence Enhanced Molecular Simulations"发表于计算化学期刊JCTC，同时当选Most Read Articles。[[论文]](https://pubs.acs.org/doi/10.1021/acs.jctc.3c00214) - `2023.5.31` NMR核磁共振动态蛋白质结构解析方法正式开源，详见论文Assisting and Accelerating NMR Assignment with Restrained Structure Prediction [[论文]](https://www.biorxiv.org/content/10.1101/2023.04.14.536890v1) [[代码]](https://atomgit.com/mindspore-lab/mindscience/tree/legacy-master/MindSPONGE/applications/research/FAAST) - `2023.1.31` MindSPONGE 1.0.0-alpha版本发布，文档介绍可参见MindSpore官网中的[**科学计算套件MindSPONGE模块**](https://mindspore.cn/mindsponge/docs/zh-CN/r1.0.0-alpha/index.html) - `2022.8.23` 论文"Few-Shot Learning of Accurate Folding Landscape for Protein Structure Prediction" arxiv预印。[[论文]](https://arxiv.org/abs/2208.09652) - `2022.07.18` 论文"SPONGE: A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms"发表于期刊Chinese Journal of Chemistry。[[论文]](https://onlinelibrary.wiley.com/doi/epdf/10.1002/cjoc.202100456) - `2022.07.09` MEGA-Assessment在CAMEO-QE月榜取得第一名 - `2022.04.21` MEGA-Fold CAMEO竞赛月榜第一。[[相关新闻]](https://www.huawei.com/cn/news/2022/4/mindspore-cameo-protein-ascend) --- ## 模型应用 ### 结构预测 #### 端到端 - 🔥AlphaFold3 [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/AlphaFold3) - 🔥Protenix [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/protenix) - 🔥RFdiffusion [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/rf_diffusion) - Alphafold-Multimer [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/afmultimer.md) - MEGAProtein [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/MEGAProtein.md) - FAAST & RASP [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/legacy-master/MindSPONGE/applications/research/FAAST) - UFold [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/UFold.md) #### 结构序列联合设计 - ProteinMPNN [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/master/MindSPONGE/applications/proteinmpnn/) - ESM-IF1 [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/ESM-IF1.md) - ColabDesign [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/ColabDesign.md) #### RNA - UFold [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/UFold.md) ### 蛋白质语言模型 - Esm2 [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/ESM-2.md) - ProtT5 [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/ProtT5.md) ### 功能与属性预测 - DeepFRI [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/DeepFri.md) - Pafnucy [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/pafnucy.md) ### 小分子与相互作用 - GROVER [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/GROVER.MD) - GraphDTA [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/GraphDTA.MD) - MGBERT [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/MGBERT.MD) - JIT-VAE[[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/legacy-master/MindSPONGE/applications/research/JT-VAE) ### 基因组/转录组语言模型 - 🔥Evo2 `In Progress` - DNABERT [[Available]](https://atomgit.com/mindspore-lab/mindscience/blob/legacy-master/MindSPONGE/applications/model_cards/DNABERT.MD) - Geneformer[[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/legacy-master/MindSPONGE/applications/research/Geneformer) ### 虚拟细胞 - 🔥MedFormer [[Available]](https://atomgit.com/mindspore-lab/mindscience/tree/legacy-master/MindSPONGE/applications/research/medformer) --- ### 分子动力学 MindSPONGE分子动力学库 (MindSpore Simulation Package tOwards Next Generation molecular modelling)是 一款基于MindSpore开发的模块化、高通量、端到端可微的下一代智能分子模拟程序库。 [[链接]](https://gitee.com/helloyesterday/mindsponge/blob/develop/README.md) --- ## 社区 ### MindSpore Science SIG [社区官网](https://www.mindspore.cn/sig/MindSpore%20Science) MindScience是基于MindSpore融合架构打造的科学计算行业套件，包含了业界领先的数据集、基础模型、预置高精度模型和前后处理工具，加速了科学行业应用开发。 ### 核心贡献者 - MindSpore AI4S Lab团队: [longyangyang](https://atomgit.com/yanglong_unimelb), [Yuheng Wang](https://atomgit.com/wyhohyw)，[chendanyang](https://atomgit.com/birfied)，[Jinxl-pp](https://atomgit.com/xianlin_jin), [wangbo](https://atomgit.com/wangbo572) - [高毅勤课题组](https://www.chem.pku.edu.cn/gaoyq/): [杨奕](https://gitee.com/helloyesterday)，[张骏](https://gitee.com/jz_90)，[刘思睿](https://gitee.com/sirui63)，[夏义杰](https://gitee.com/xiayijie)，[陈迪青](https://gitee.com/dechin)，[刘许晗](https://gitee.com/XuhanLiu) ### 合作伙伴
     
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