Structural Models

Lecture 11

Structural Models: Introduction

Structural models display relationships among entities and have a variety of uses, such as

• viewing interpretations of data in multiple dimensions;

• representing an idealized structure and data that are mapped to its coordinates;

• identifying analogous structures across entities or organisms; and

• analyzing structures to infer properties.

Researchers have developed informatics tools for a variety of disciplines best represented by geological and biology.

Structural Models: Historical Use

• Watson and Crick• Bohr’s Model of the Atom• others…

Geographical Modeling: RockWorks

RockWorks is a rich environment for modeling the Earth’s crust given spatially distributed data (e.g., from boreholes).

RockWorks interpolates observations to display stratigraphic models of the Earth’s crust.

Brain Explorer

Brain Explorer displays 2D and 3D models of the Allen Brain Atlas for mice.

Brain Explorer: Overlay

Brain Explorer primarily supports browsing the atlas and overlaying gene expression levels on the model.

Gene expression levels overlaid on the hippocampus.

EcoCyc

EcoCyc is a repository of knowledge about the E. coli bacterium and is part of the larger BioCyc collection.

The interface is web based and supports knowledge retrieval, data interpretation, and comparative analysis.

EcoCyc: Content

EcoCyc contains detailed information on

• the genome for E. coli and other organisms;

• the metabolic pathways for E. coli;

• the corresponding reactions and compounds.

EcoCyc: Structure Alignment

A key feature is the ability to align genome models from various species centered on specific genes.

Here, genomes for E. coli, Salmonella, and Chlamydia are aligned around the gene for the TyrB protein.

EcoCyc: Summary

The structural models in EcoCyc let researchers

• browse a vast collection of information using their own knowledge of biological organisms;

• compare the genomes of multiple organisms to identify structural and functional analogs; and

• access data and research articles associated with the repository’s primary content.

UCSF Chimera

UCSF Chimera supports molecular visualization, structural comparison, and structural analysis.

The software lets scientists produce high quality images and animation of their models and corresponding analyses.

UCSF Chimera: Bond Detection

Chimera can identify hydrogen bonds based on the distances between atoms (shown in pink below).

UCSF Chimera: Structure Alignment

Chimera also aligns different models of the same molecule (here an enzyme from Staphylococcus aureus)

The models, colored magenta and white, differ in the region marked by the arrow.

UCSF Chimera: Summary

UCSF Chimera lets scientists carry out several tasks related to molecular models including

• view interactive models of molecular structure;

• integrate models and data from multiple sources (e.g., electron microscope maps, protein data bank models);

• compute model properties, including 3D surfaces, implied by component atoms and their positions; and

• analyze similarities and differences among models.

Structural Modeling: Summary

The software presented in this lecture shared several common features, such as

• they often generate structural models by processing data with predefined algorithms;

• they provide access to distributed databases from within the application or web interface; and

• they focus on comparative analysis either among structures or among data sets mapped to the structures.

These features expand the usefulness of structural models to support complex entities and to facilitate collaboration.