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A knowledge-based system for macromolecular model building and evaluation.

机译：基于知识的大分子模型建立和评估系统。

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摘要

This dissertation focuses on the development and application of automated methods to help biologists model the structure of macromolecular complexes from experimentally derived structural information and evaluate proposed models. In particular, we assert that general purpose knowledge-based systems can support the construction and evaluation of models. For RIBOWEB, the prototype system, we use the macromolecular complex of the ribosome as the domain.; In this document, we describe the RIBOWEB system and present our work applying RIBOWEB functionality to the construction of tRNA models in the ribosome and the evaluation of several ribosomal models and crystal structures with respect to published experimental structural data. We show that a knowledge-based system can indeed be used to support macromolecular modeling and evaluation.; We propose a model of A-site and P-site tRNAs in the ribosome based solely on experimental structural information. We found that valuable structural information for modeling can be generated by tethered hydroxyl radical probing experiments. Our tRNA model was created before the high-resolution crystal structure was available and is in agreement with it though created from totally independent data.; We also provide an evaluation of the applicability and reliability of experimental structural information for low resolution ribosomal modeling. We performed comparisons of ribosomal models with experimental structural information and identified several characteristics of experimental data that could be useful for future modeling. These characteristics include large amounts of variation in structural information from crosslinking experiments and large distance ranges represented by structural information from footprinting experiments. We also performed comparisons of ribosomal crystal structures with experimental structural information. We found that most distances in the ribosome derived from experimental structural information were small, but that the distribution of distances was quite large, implying that loose distance assignments to experimental data is important when modeling with experimental data from multiple sources.
机译：本文致力于自动化方法的开发和应用，以帮助生物学家从实验得出的结构信息中建模高分子复合物的结构并评估所提出的模型。特别是，我们认为基于通用知识的系统可以支持模型的构建和评估。对于原型系统RIBOWEB，我们使用核糖体的大分子复合物作为结构域。在本文档中，我们描述了RIBOWEB系统，并介绍了将RIBOWEB功能应用于核糖体中tRNA模型的构建以及相对于已发表的实验结构数据的几种核糖体模型和晶体结构的评估的工作。我们表明，基于知识的系统确实可以用于支持大分子建模和评估。我们仅基于实验结构信息提出了核糖体中A位和P位tRNA的模型。我们发现可以通过拴系的羟基自由基探测实验来生成有价值的建模信息。我们的tRNA模型是在高分辨率晶体结构可用之前创建的，尽管它是从完全独立的数据创建的，但与它一致。我们还提供了针对低分辨率核糖体建模的实验结构信息的适用性和可靠性的评估。我们将核糖体模型与实验结构信息进行了比较，并确定了可用于将来建模的实验数据的几个特征。这些特征包括来自交联实验的结构信息的大量变化，以及来自足迹实验的结构信息所代表的大距离范围。我们还进行了核糖体晶体结构与实验结构信息的比较。我们发现，核糖体中来自实验结构信息的大多数距离很小，但是距离的分布却很大，这意味着在对来自多个来源的实验数据进行建模时，分配给实验数据的距离很重要。

著录项

  • 作者

    Carrillo, Michelle Whirl.;

  • 作者单位

    Stanford University.;

  • 授予单位 Stanford University.;
  • 学科 Biophysics General.
  • 学位 Ph.D.
  • 年度 2003
  • 页码 156 p.
  • 总页数 156
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物物理学;
  • 关键词

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