RAPID: MolSSI COVID-19 Biomolecular Simulation Data and Algorithm Consortium

为应对日益严重的COVID-19疫情，分子科学软件研究所（MolSSI）将利用其作为中立商品资源的地位，帮助全球计算分子科学界快速提供科学数据和专业知识，以应对COVID-19危机。MolSSI由高级网络基础设施办公室和化学与材料研究部门共同支持。这项工作的核心将是（1）针对病毒和宿主蛋白质以及潜在药物的模拟相关数据的集中存储库，以及（2）一组精选的MolSSI软件种子奖学金。学生和博士后针对COVID-19相关的软件工具，这些软件工具对存储库中开发的数据进行操作。 这两个组件将使生物分子模拟社区能够共享和利用关键数据和其他资源，以帮助识别宿主-病毒复合物的结构和动态特征，从而产生潜在的治疗线索。 虽然该项目旨在解决严重的COVID-19危机，但在短期内，它也将影响研究社区和下一代计算分子科学家对抗和主动解决未来世界问题。MolSSI将创建和管理一个大规模的存储库，包含：模拟输入文件（结构，配置，脚本，笔记本电脑）在一个有组织的结构; MD轨迹，分析工具，并准备好模型的药物发现;关于SARS-CoV-2生物分子模拟研究的预印本服务器（如arXiv、bioRxiv和ChemRxiv）的指针;以及创建可引用数据的DOI服务。 此外，它还将通过一系列针对研究生和博士后的软件奖学金来吸引分子科学界的参与，以进行软件开发，例如大规模MD模拟，药物发现工具的设计，例如对接，用于小分子毒性预测的机器学习，以及确定新药是否具有生物利用度或可以合成的方法。 总的来说，这些资源将加速抗病毒药物的鉴定和开发，分析SARS-CoV-2病毒遗传变异的结构效应，和抑制剂，可以破坏蛋白质-蛋白质相互作用，病毒进入细胞和粘附表面，导致疾病传播。这个奖项是由关怀法案补充资金分配给CISE和MPS资助。这个奖项反映了NSF的法定使命，通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

In response to the growing COVID-19 pandemic, the Molecular Sciences Software Institute (MolSSI) will leverage its position as a neutral commodity resource to help the global computational molecular sciences community quickly provide their scientific data and expertise to address the COVID-19 crisis. The MolSSI is jointly supported by the Office of Advanced Cyberinfrastructure and the Divisions of Chemistry and Materials Research. The centerpieces of this engagement will be (1) a centralized repository for simulation-related data targeting the virus and host proteins and potential pharmaceuticals, and (2) a select set of MolSSI Software Seed Fellowships for Ph.D. students and postdocs targeting COVID-19 related software tools that operate on the data developed in the repository. These two components will enable the biomolecular simulation community to share and utilize key data and other resources to help identify the structural and dynamic characteristics of the host-virus complex to generate potential leads for therapeutics. Although this project is intended to address the acute COVID-19 crisis, in the near term, it also will impact research communities and the next generation of computational molecular scientists in the confrontation and proactive resolution of future world problems.The MolSSI will create and curate a large-scale repository containing: simulation input files (structures, configurations, scripts, Jupyter notebooks) in an organized structure; MD trajectories, analysis tools, and ready models for drug discovery; pointers to preprint servers such as arXiv, bioRxiv, and ChemRxiv on biomolecular simulation research in regards SARS-CoV-2; and DOI services that create citable data. In addition, it will engage the molecular sciences community through a set of Software Fellowships for graduate student and postdocs to carry out software development, such as large-scale MD simulations, design of drug discovery tools such as docking, machine learning for small molecule toxicity predictions, and methods for determining whether new drugs are bioavailable or can be synthesized. Collectively, these resources will speed the identification and development of leads for antiviral drugs, analyzing structural effects of genetic variation in the SARS-CoV-2 virus, and inhibitors that can disrupt protein-protein interactions to viral entry into cells and adherence to surfaces that cause disease spread.This award is being funded by the CARES Act supplemental funds allocated to CISE and MPS.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.