Structural Bioinformatics Preview: Chapter 1 结构生物信息学
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Defining Bioinformatics and Structural Bioinformatics

what is bioinformatics?

Some define it narrowly as the development of databases to store and manipulate genomic information. Others define it broadly as encompassing all of computational biology.

structural bioinformatics catalyzed by large amounts of data

结构生物信息学肇始于DNA结构和蛋白质晶体结构的发现,通过NMR、X射线衍射等手段进行研究。
基因组计划 Genome-sequencing projects 的成功,为结构生物信息学带来了新的活力。现今的结构生物信息学综合使用多种手段,由庞大的数据支持和驱动。

Toward a High-Resolution Understanding of Biology

Bioinformatics has certain promises that promote biology research.

The promise for structural bioinformatics lies in four areas: (1) creating an infrastructure for building up structural models from component parts; (2) gaining the ability to understand the design principles of proteins so that new functionalities can be created; (3) learning how to design drugs efficiently based on structural knowledge of their target; and (4) catalyzing the development of simulation models that can give insight into function based on structural simulations.

Rational Drug Design

It has not been the primary way of discovering new therapeutics. One of the greatest success is the creation of HIV protease inhibitors based on the known 3D structure.

Methods for matching combinatorial libraries of chemicals against protein binding sites have matured and are in routine use at most pharmaceutical companies.

Technical challenges within structural bioinformatics

结构生物信息学主要有两大发展方向:creating methods to support biology and structural genomics; creating methods to elucidate 阐明 new biological knowledge. 其中需要用到多种informatics approaches:

  1. Target selection
  2. Tracking experimental crystallization trials
  3. Analysis of crystallographic data
  4. Analysis of NMR data
  5. Assessment and evaluation of structures
  6. Storing molecular structures in databases
  7. Correlating molecular structural information with structural and functional information gained from other types of experimentation

Understanding the structural basis for biological phenomenon

Given the structural information created by efforts in X-ray crystallography and NMR, there are a wide range of analytic and scientific challenges to informatics. It is not possible to cover the full scope of activities, but they can be reviewed briefly to show the richness of opportunities in the analysis of structural data.

  • visualization
  • classification
  • prediction
  • simulation

参考文献:

Bourne, P. E., & Weissig, H. (2003). Structural bioinformatics.

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