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:
- A. Šali and T. L. Blundell. Comparative protein modelling by satisfaction of
spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
- 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.
- 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.
- 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.
- A. Fiser, R. K. G. Do and A. Šali.
Modeling of loops in protein structures.
Protein Science 9, 1753-1773, 2000.
- F. Melo, R. Sánchez, A. Šali. Statistical potentials for fold assessment.
Protein Science 11, 430-448, 2002.
- 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.
- 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.
- 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.
- 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.