MACROMOLECULAR PATTERN RECOGNITION & ONLINE ACCESS TO MOLEC BIOL TOOLS: DNA SEQ

大分子模式识别

• 批准号: 6469053
• 负责人: MICHAEL GRIBSKOV
• 金额: $ 10.66万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-06-01 至 2002-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6469053
• 关键词: biological products; biomedical resource; computers; nucleic acids; proteins; technology /technique

In 1997/1998 activities in this core project were focused on i) validation of the DMol/COSMO program and ii) supporting use of the program at SDSC. i) Several validation projects were accomplished and results were presented as invited contributions at major international conferences. The influence of solvent on structures and relative energies of various conformers such as betaines and sulfobetaines, ethers, carboxylic acids, aldehydes and ketones was studied using the DMol/COSMO model. Organic reactions including: dipolar cycloadditions, parent Diels-Alder reactions, keto-enol tautomerism, ring opening of cyclobutene, proton exchange in amides and radical addition reactions were studied. The effect of solvent on the transition state and enthalpy of reactions was elucidated. In some cases it was found necessary to include the water molecules explicitly in quantum calculations, while the remaining solvent was represented as a dielectric continuum. Dmol/COSMO approach was used to evaluate the free energies of hydration for over 150 small to medium size molecules, cations and anions. A significant validation study of DMol/COSMO method augmented with the COSMO-RS model was done. Results of vapor pressure, surface tension, partition coefficients for over 200 molecules demonstrate a practical utility of the DMol/COSMO/COSMO-RS model. ii) The DMol/COSMO methodology was presented at an SDSC workshop. Collaboration with personnel of SDSC was enhanced. In particular, support in using DMol/COSMO program was provided to Drs. Igor Tsigelny and Lynn Ten Eyck in their research on conformations of methylphosphonothioates. As a first step, the optimized structures of 6 organophosphonate pairs, were calculated using DMol/COSMO program in gas phase and in water. Relative energies of conformers were found and the charge distribution due to the solvent effects was calculated. Further calculations are planned to estimate the transition states of such OP reactions with active serine of AchE and other esterases.

1997/1998年，这一核心项目的活动侧重于： DMol/COSMO计划的验证，以及ii）支持使用 SDSC的计划。 （一）完成了几个验证项目， 结果作为邀请的贡献在主要国际会议上发表， 两会 溶剂对结构及相关性质的影响 各种构象异构体如甜菜碱和磺基甜菜碱的能量， 醚，羧酸，醛和酮的研究使用的 DMol/COSMO模型。 有机反应包括：偶极反应 环加成，母体Diels-Alder反应，酮-烯醇互变异构， 环丁烯开环，酰胺质子交换和自由基 研究了加成反应。 溶剂对反应的影响 反应的过渡态和反应焓。 在一些 在某些情况下，发现有必要明确地包括水分子， 在量子计算中，当剩余的溶剂被表示为 作为电介质连续体。 采用Dmol/COSMO方法评价 超过150个小到中等尺寸的水化自由能 分子、阳离子和阴离子。 一项重要的验证研究， 用COSMO-RS模型对DMol/COSMO方法进行了补充。 结果 蒸汽压，表面张力，分配系数 200个分子证明了 DMol/COSMO/COSMO-RS模型。 2. DMol/COSMO方法 参加SDSC研讨会。 与SDSC人员的合作 被增强了。 特别是，支持使用DMol/COSMO程序， 提供给Igor Tsigelny和林恩滕艾克博士在他们的研究， 甲基硫代膦酸酯的构象。 作为第一步 计算了6种有机膦酸酯对的优化结构 用DMol/COSMO程序在气相和水中进行计算。 相对能量 的构象被发现和电荷分布，由于 计算溶剂效应。 计划进行进一步计算， 估计具有活性丝氨酸的此类OP反应的过渡态 乙酰胆碱酯酶和其他酯酶。