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

大分子模式识别

• 批准号: 6324793
• 负责人: MICHAEL GRIBSKOV
• 金额: $ 30.53万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-05-01 至 2001-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6324793
• 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集中在1) DMOL/COSMO计划的验证和ii)支持使用 计划在SDSC。一)完成了几个验证项目， 成果作为特邀稿件在大型国际会议上发表。 会议。溶剂对结构和相对分子质量的影响 各种构象的能量，如甜菜碱和磺基甜菜碱， 对醚、羧酸、醛和酮进行了研究 DMOL/COSMO模型。有机反应包括：偶极反应 环加成反应，母体Diels-Alder反应，酮-烯醇互变异构， 环丁烯的开环、酰胺和自由基中的质子交换 对加成反应进行了研究。溶剂对紫外光照射的影响 阐明了反应的过渡态和反应热。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，当剩余溶剂被表示时 作为一个介电连续体。采用DMOL/COSMO方法进行评价 150多种中小型矿物的水化自由能 分子、阳离子和阴离子。一项重要的验证研究 在COSMO-RS模型的基础上进行了DMOL/COSMO方法的改进。结果 蒸汽压，表面张力，分配系数 200个分子展示了一种实用的 DMOL/COSMO/COSMO-RS模型。二)DMOL/COSMO方法是 在SDSC研讨会上发表。与SDSC的人员协作 得到了增强。特别是，对使用DMOL/COSMO方案提供了支持 提供给Igor Tsigelny博士和Lynn Ten Eyck博士 甲基硫代亚膦的构象。作为第一步， 对6个有机膦酸盐对进行了结构优化计算 在气相和水中使用DMOL/COSMO程序。相对能量 发现了构象的数量和电荷分布 计算了溶剂效应。计划进行进一步的计算 用活性丝氨酸估算这类OP反应的过渡态 酸痛和其他酯酶。