Comparative protein structure modeling with MODELLER:
A practical approach

András Fiser and Andrej Sali



Laboratories of Molecular Biophysics
Pels Family Center for Biochemistry and Structural Biology
The Rockefeller University
1230 York Avenue, New York, NY 10021, USA








Correspondence to Andrej Sali
The Rockefeller University
1230 York Avenue, New York, NY 10021, USA
tel: +1 (212) 327 7550; fax: +1 (212) 327 7540
e-mail: sali@rockefeller.edu


Running title: Comparative protein structure modeling

 

• Introduction
• Comparative modeling steps
  • Searching for structures related to the target sequence
  • Selecting templates
  • Aligning the target sequence with one or more structures
  • Model Building
  • Evaluating a model
  • Iterating alignment, modeling and model evaluation
• Modeling examples using MODELLER
  • Example 1: Modeling lactate dehydrogenase from Trichomonas vaginalis based on a single template
    • Searching for structures related to TvLDH
    • Selecting a template
    • Aligning TvLDF with the template
    • Model building
    • Evaluating a model
  • Example 2: Modeling of a protein-ligand complex based on multiple templates and user specified restraints
  • Example 3: Modeling the fold and a loop in circularly permuted cyanovirin
• Bibliography
• About this document ...