TriadWeb: An easy-to-use web-based platform for protein engineering.

TriadWeb：一个易于使用的基于网络的蛋白质工程平台。

• 批准号: 8834160
• 负责人: Barry D Olafson
• 金额: $ 15万
• 依托单位: PROTABIT, LLC
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2015-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8834160
• 关键词: Address; Algorithms; Amino Acid Sequence; Area; Back; Biological Assay; Biology; Cellular Phone; Cloud Computing; Collaborations; Communication; Complex; Computer software; Data; Development; Development Plans; Diagnostic Reagent; Disease; Employee; Engineering; Environment; Enzymes; Goals; Graph; Healthcare; Human; Imagery; Industry; Internet; Intranet; Knowledge; Laboratories; Learning; Libraries; Link; Maintenance; Marketing; Medicine; Metabolic Diseases; Methods; Modeling; Molecular; Monoclonal Antibodies; Online Systems; Peptide Sequence Determination; Pharmaceutical Preparations; Pharmacologic Substance; Phase; Positioning Attribute; Procedures; Property; Protein Engineering; Proteins; Protocols documentation; Recording of previous events; Research; Research Infrastructure; Risk; Running; Sales; Science; Scientist; Secure; System; Technology; Testing; Therapeutic; Therapeutic antibodies; TimeLine; Translating; Triad Acrylic Resin; Validation; Variant; base; cancer therapy; cloud based; commercial application; computerized tools; computing resources; design; drug discovery; encryption; experience; flexibility; graphical user interface; improved; meetings; novel; novel diagnostics; prevent; protein complex; public health relevance; screening; simulation; small molecule; therapeutic protein; tool; web services; web site

DESCRIPTION (provided by applicant): Monoclonal antibodies and other protein-based therapeutics represent a $100+ billion and growing market with broad applications in the treatment of cancer, metabolic diseases, and other human disorders. Thus, any technology that facilitates the discovery of useful protein variants will have a major impact in biology and medicine; application areas include drug discovery, small molecule screening, and the development of new diagnostics and reagents. One such enabling technology that has been under active development in the last decade is computational protein design (CPD). Current CPD platforms are highly flexible, powerful, and capable of performing a wide range of functions. However, these platforms are also complicated and difficult to use, requiring significant knowledge to be wielded effectively. In addition, they require specialized software and hardware systems, which places a high technical burden on installation and maintenance for non-expert users. All these factors make it unlikely that CPD will become a standard tool for experimentalists who want to engineer novel proteins. In order to make CPD accessible to bench scientists, Protabit will develop a web-based, easy-to-use, commercial platform for protein engineering called TriadWeb. This web-based platform will build on Triad, Protabit's existing software suite for protein engineering, which was developed in collaboration with Caltech and Monsanto. The objectives of this Phase I project are: (1) develop a suite of web-based "apps" that harness the full power of CPD in a simple, easy-to-understand way; (2) develop the back-end software infrastructure to enable a cloud-based web-service with user authentication and encryption; (3) couple TriadWeb with a secure, user-partitioned dataserver to assist in the organization, sharing, and querying of project data; and (4) incorporate dynamic, interactive visualization tools to assist in viewing and interpreting data and results. With TriadWeb, the web browser will gather the minimal necessary input needed to suggest new protein sequence libraries that can then be expressed and assayed in the lab for desired properties. This input will be gathered using concepts readily understandable to bench scientists. TriadWeb will convert these high level directives into complex protein design simulations, all running on specialized hardware maintained either by Protabit or in a cloud environment. The results will be provided visually to the bench scientist in the form of 3D molecular renderings, charts and graphs where possible. Fortunately, the field of CPD has advanced to the point where many CPD functions can be packaged as "applications" in much the same manner as the applications that are routinely found on smart phones and iPads. The overall objective of this Phase I proposal and the follow-on Phase II proposal is to provide bench scientists with a usable suite of "apps" that translate complex CPD functions into simple easy-to-learn procedures.

描述（由申请人提供）：单克隆抗体和其他基于蛋白质的治疗剂代表了1000多亿美元的不断增长的市场，在癌症、代谢疾病和其他人类疾病的治疗中具有广泛的应用。因此，任何有助于发现有用蛋白质变体的技术都将对生物学和医学产生重大影响;应用领域包括药物发现，小分子筛选以及新诊断和试剂的开发。在过去十年中一直在积极发展的一种这样的使能技术是计算蛋白质设计（CPD）。当前的CPD平台高度灵活、功能强大，能够执行广泛的功能。然而，这些平台也很复杂，难以使用，需要大量的知识才能有效地运用。此外，它们需要专门的软件和硬件系统，这给非专业用户的安装和维护带来了很大的技术负担。所有这些因素使得CPD不太可能成为想要设计新蛋白质的实验者的标准工具。为了使CPD能够被实验室科学家使用，Protabit将开发一个基于网络的、易于使用的蛋白质工程商业平台，称为TriadWeb。这个基于网络的平台将建立在Protabit现有的蛋白质工程软件套件Triad的基础上，该软件套件是与加州理工学院和孟山都公司合作开发的。该第一阶段项目的目标是：（1）开发一套基于网络的“应用程序”，以简单、易于理解的方式利用CPD的全部功能;（2）开发后端软件基础设施，以启用具有用户身份验证和加密的基于云的网络服务;（3）将TriadWeb与一个安全的、用户分区的Web服务器相结合，以帮助组织、共享和查询项目数据;以及（4）结合动态、交互式可视化工具以帮助查看和解释数据和结果。使用TriadWeb，Web浏览器将收集建议新蛋白质序列库所需的最小必要输入，然后可以在实验室中表达和分析所需特性。将使用实验室科学家易于理解的概念收集这些输入。TriadWeb将这些高级指令转换为复杂的蛋白质设计模拟，所有这些都在Protabit或云环境中维护的专用硬件上运行。结果将以3D分子渲染图、图表和图形（如可能）的形式直观地提供给实验室科学家。幸运的是，CPD领域已经发展到许多CPD功能可以以与智能手机和iPad上常见的应用程序大致相同的方式打包为“应用程序”的地步。第一阶段提案和后续第二阶段提案的总体目标是为实验室科学家提供一套可用的“应用程序”，将复杂的CPD功能转化为简单易学的程序。

项目成果

ProtaBank: A repository for protein design and engineering data.

ProtaBank：蛋白质设计和工程数据的存储库。

• DOI: 10.1002/pro.3585
• 发表时间: 2019
• 期刊: Protein science : a publication of the Protein Society
• 作者: Wang,ConnieY;Chang,PaulM;Ary,MarieL;Allen,BenjaminD;Chica,RobertoA;Mayo,StephenL;Olafson,BarryD
• 通讯作者: Olafson,BarryD