WEB BASED DOCUMENTATION & TUTORIALS FOR YAMMP

基于网络的文档

• 批准号: 6283168
• 负责人: STEPHEN C. HARVEY
• 金额: $ 2.49万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-06-15 至 1999-06-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6283168
• 关键词: biomedical resource; computers; structural biology; technology /technique

Adequate on-line documentation is a great asset for any widely used molecular modeling package. Since YAMMP was originally developed only for use at the University of Alabama at Birmingham (UAB), documentation had not previously been regarded as a critical issue. With the establishment of this Research Resource and a series of new collaborations with scientists outside UAB, proper documentation became a high priority. We decided to take advantage of web technology, and we have begun developing complete on-line documentation for YAMMP. From the beginning, we have coupled the documentation to a series of on-line tutorials for educating new users in the principles and practices of using YAMMP for modeling macromolecular systems. The tutorial package has modules aimed at experienced modelers and structural biologists: these focus on the empirical force field used in low resolution YAMMP models. Another set of modules is aimed at the novice modeler: these use simple alkanes to teach the basic principles of molecular mechanics, including force fields and algorithms (energy minimization; molecular dynamics; Monte Carlo; simulated annealing). Since the tutorials assume certain basic mathematical skills, we are also developing tutorials to help students refresh or learn those skills as necessary: these include such concepts as the normal distribution, the Boltzmann distribution, Fourier analysis, and so on.

充足的在线文档对于任何广泛使用的人来说都是一笔宝贵的财富。 使用分子建模包。 由于 YAMMP 最初是开发出来的 仅供阿拉巴马大学伯明翰分校 (UAB) 使用， 文档以前并不被视为一个关键问题。 随着该研究资源的建立和一系列新的 与 UAB 以外的科学家合作、适当的文档 成为当务之急。 我们决定利用网络 技术，我们已经开始开发完整的在线 YAMMP 的文档。 从一开始，我们就将 用于教育新用户的一系列在线教程的文档 使用YAMMP进行建模的原理和实践 大分子系统。 该教程包的模块旨在 经验丰富的建模师和结构生物学家：他们专注于 低分辨率 YAMMP 模型中使用的经验力场。 其他 模块集针对新手建模者：这些模块使用简单 烷烃教授分子力学的基本原理， 包括力场和算法（能量最小化；分子 动力学;蒙特卡洛；模拟退火）。 自从有了教程 假定某些基本的数学技能，我们也在发展 帮助学生根据需要刷新或学习这些技能的教程： 其中包括正态分布、玻尔兹曼分布等概念 分布、傅里叶分析等。