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MODELLER bibliography

In your publications using MODELLER, please quote

A. Šali and T. L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

More information about the methods implemented in MODELLER, their use, applications, and limitations can be found in the papers listed on our web site at `https://salilab.org/publications/`. Here is a subset of these publications:

1. A. Šali and T. L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

2. A. Šali and J. P. Overington. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science 3, 1582-1596, 1994.

3. R. Sánchez and A. Šali. Comparative protein structure modeling: Introduction and practical examples with MODELLER. In Protein Structure Prediction: Methods and Protocols, D.M. Webster, editor, 97-129. Humana Press, 2000.

4. M. A. Martı-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo and A. Šali. Comparative protein structure modeling of genes and genomes. Ann. Rev. Biophys. Biomolec. Struct. 29, 291-325, 2000.

5. A. Fiser, R. K. G. Do and A. Šali. Modeling of loops in protein structures. Protein Science 9, 1753-1773, 2000.

6. F. Melo, R. Sánchez, A. Šali. Statistical potentials for fold assessment. Protein Science 11, 430-448, 2002.

7. M. A. Martı-Renom, B. Yerkovich, and A. Šali. Comparative protein structure prediction. John Wiley & Sons, Inc. Current Protocols in Protein Science 1, 2.9.1 - 2.9.22, 2002.

8. U. Pieper, N. Eswar, A. C. Stuart, V. A. Ilyin and A. Šali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30, 255-259, 2002.

9. A. Fiser and A. Šali. MODELLER: generation and refinement of homology-based protein structure models. In Methods in Enzymology, C.W. Carter and R.M. Sweet, eds. Academic Press, San Diego, 374, 463-493, 2003.

10. N. Eswar, B. John, N. Mirkovic, A. Fiser, V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Martı-Renom, M. S. Madhusudhan, B. Yerkovich and A. Šali. Tools for comparative protein structure modeling and analysis. Nucleic Acids Research 31, 3375-3380, 2003.