Comparative Protein Structure Modeling

Addendum to:
Comparative Protein Structure Modeling:
Introduction and practical examples with MODELLER

This page contains example files and software links for the chapter "Comparative Protein Structure Modeling: Introduction and practical examples with MODELLER" which is included in the book "Protein Structure Prediction: Methods and Protocols" (David M. Webster, editor) published by Humana Press, Inc. as part of their "Methods In Molecular Biology" series. The manuscript is also available.

Example files

All files have the same names as in the text. The MODELLER manual can be accessed here. Please note that these examples have been updated to work with Modeller 7v7; the original files used in the manuscript (which worked with Modeller 4h) are also available.

• Example 1 : Modeling with a single template.
• Example 2 : Modeling of a protein/ligand complex.
• Example 3 : Modeling based on more than one template.
• Example 4 : The alignment-modeling-evaluation cycle.

Software list

An updated list of the links from Table 2 of the text can be found at our lab's bioinformatics resources page.