NEW! Our Homology Model Construction Server uses the MODELLER software (salilab.org/modeller) to "build" structures from sequences (of unknown structure) by using homologous proteins of known structure.
We are working to improve the quality of the predicted models by incorporating phylogetic tree construction and sequence/structure analysis into the template selection, alignment and constraint estimation process.
This paper is a good introduction to MODELLER. It includes examples of its use:
R. Sánchez, A. Sali. Comparative protein structure modeling: Introduction and practical examples with MODELLER. In: Protein Structure Prediction: Methods and Protocols. Ed: D. M. Webster. Humana Press, 97-129, 2000.
This paper is also available at http://guitar.rockefeller.edu/pdf/080_SanMethods2000.pdf