Evolutionary Analysis of Protein using HyperChem

描述(申请人提供)：在第二阶段结束时，我们将推出一款新的商业产品：HYPERPROTEIN。HYPERPROTEIN将建立在现有的软件平台HYPERCHEM上，目前HYPERCHEM的商业版本为7.5。HYPERCHEM用于教育和工业，将分子建模和计算化学应用于分子。在第一阶段已经确定了将HYPERPROTEIN产品放在HYPERCHEM平台上的可行性，这既是通过实现第一阶段提案中给出的目标，也是通过对芳香酶蛋白质家族的系统基因组分析。第二阶段的具体科学目标是扩大我们对系统基因组学工具的理解，以便更好地在产品中放置替代工具。技术上的特定目标是执行支持这些工具所需的软件工程。教育的具体目标将制定手册和教程，描述系统发育学工具的使用。这将包括一系列工作的例子，说明先进的系统基因组分析的应用。通过软件工程出现的HYPERPROTEIN产品将协助目标1和3，这需要基金会科学家和HyperCube工作人员之间的合作，他们将主要负责目标1和3，超级立方体工作人员将主要负责目标2。 HYPERPROTEIN将满足教育软件市场的需求：今天，没有面向教育的产品支持化学、系统基因组和结构生物学分析。通过将HYPERCHEM的能力扩展到生物分子科学，HYPERPROTEIN预计将使其在教育市场的订阅基数翻两番，并扩大其在工业中的使用。在未来，应该有可能通过将该产品连接到自然组织的蛋白质序列数据库来进一步增强该产品。这将确保其作为一个完整的系统基因组学软件包在学术和工业领域取得商业成功。

DESCRIPTION (provided by applicant): At the end of Phase II, we will launch a new commercial product: HYPERPROTEIN. HYPERPROTEIN will be built on an existing software platform, HYPERCHEM, now in its commercial Version 7.5. HYPERCHEM is used in both education and industry to apply molecular modeling and computational chemistry to molecules. The feasibility of placing the HYPERPROTEIN product on the HYPERCHEM platform has been established in Phase I, both by meeting the Aims given in the Phase I proposal, and through a phylogenomic analysis of the aromatase family of proteins. The scientific Specific Aim of Phase II is to expand our understanding of phylogenomics tools to better place alternative tools in the product. The technological Specific Aim is to perform the software engineering required to support these tools. The educational Specific Aim will develop manual and tutorial describing the use of phylogenomic tools. This will include a series of worked examples that illustrate the application of advanced phylogenomic analysis. The HYPERPROTEIN product, as it emerges through software engineering, will assist with Aims 1 and 3, requiring collaboration between the Foundation scientists, who will be primarily responsible for Aims 1 and 3, and HyperCube staff, who will be primarily responsible for Aim 2. HYPERPROTEIN will fill a need in the educational software market: today, no educationally oriented product supports chemical, phylogenomic, and structural biological analysis. By expanding the capabilities of HYPERCHEM towards the biomolecular sciences, HYPERPROTEIN is expected to quadruple its subscription base in the educational market, and expand its use in industry. In the future, it should be possible to further enhance the product by joining it to naturally organized protein sequence databases. This should ensure its commercial success as an integrated phylogenomics software package, in both the academic and industrial sectors.