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MODELLER bibliography

More information about MODELLER and its applications can be found in the following sources:

  1. Šali, A. and Blundell, T. L. Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403-428 (1990).

  2. Šali, A., Overington, J. P., Johnson, M. S., and Blundell, T. L. From comparisons of protein sequences and structures to protein modelling and design. TIBS 15, 235-240 (1990).

  3. Johnson, M. S., Šali, A., and Blundell, T. L. Phylogenetic relationships from three-dimensional protein structures. Meth. Enzymol. 183, 670-690 (1990).

  4. Johnson, M. S., Overington, J. P., and Šali, A. Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin. In Current Research in Protein Chemistry: Techniques Structure and Function, Villafranca, J. J., editor, 567-574. Academic Press, Inc., San Diego (1990).

  5. Šali, A. Modelling three-dimensional structure of proteins from their sequence of amino acid residues. PhD thesis, University of London, London, (1991).

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

  7. Šali, A., Matsumoto, R., McNeil, H. P., Karplus, M., and Stevens, R. L. Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes. J. Biol. Chem. 268, 9023-9034 (1993).

  8. Šali, A. and Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. In Protein Structure by Distance Analysis, Bohr, H. and Brunak, S., editors, 64-86. IOS Press, Amsterdam (1994).

  9. Šali, A. and Overington, J. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3, 1582-1596 (1994).

  10. Šali, A. MODELER: Implementing 3D protein modeling. In $mc^2$, volume 2, 5. Molecular Simulations Inc., Burlington, MA (1995).

  11. Matsumoto, R., Šali, A., Ghildyal, N., Karplus, M., and Stevens, R. L. Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines in mouse mast cell protease-7 regulates its binding to heparin serglycin proteoglycan. J. Biol. Chem. 270, 19524-19531 (1995).

  12. Šali, A. Protein modeling by satisfaction of spatial restraints. Molecular Medicine Today 1, 270-277 (1995).

  13. Šali, A., Potterton, L., Yuan, F., van Vlijmen, H., and Karplus, M. Evaluation of comparative protein structure modeling by MODELLER. Proteins 23, 318-326 (1995).

  14. Šali, A. Modelling mutations and homologous proteins. Curr. Opin. Biotech. 6, 437-451 (1995).

  15. Sheng, Y., Šali, A., Herzog, H., Lahnstein, J., and Krilis, S. Modelling, expression and site-directed mutagenesis of human $\beta_2$-glycoprotein I: Identification of the major phospholipid binding site. J. Immunol. 157, 3744-3751 (1996).

  16. Ghildyal, N., Friend, D. S., Stevens, R. L., Austen, K. F., Huang, C., Penrose, J., Šali, A., and Gurish, M. F. Fate of two mast cell tryptases following passive systemic anaphylaxis of BALB/c and V3 mastocytosis mice. Prolonged retention of exocytosed mMCP-6 in connective tissues and rapid accumulation of enzymatically active mMCP-7 in the blood chymases. J. Exp. Med. 184, 1061-1073 (1996).

  17. Xu, L. Z., Sánchez, R., Šali, A., and Heintz, N. Ligand specificity of brain lipid binding protein. J.Biol.Chem. 271, 24711-24719 (1996).

  18. Wu, S., de Lencastre, H., Šali, A., and Tomasz, A. A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: Molecular cloning and DNA sequencing. Microbial Drug Resistance 2, 277-286 (1996).

  19. Huang, C., Wong, G. W., Ghildyal, N., Gurish, M. F., Šali, A., Matsumoto, R., Qiu, W.-T., and Stevens, R. L. The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma. J. Biol. Chem. 272, 31885-31893 (1997).

  20. Sánchez, R. and Šali, A. Comparative protein modeling as an optimization problem. Journal of Molecular Structure (Theochem) 398, 489-496 (1997).

  21. Sánchez, R. and Šali, A. Advances in comparative protein-structure modeling. Curr. Opin. Struct. Biol. 7, 206-214 (1997).

  22. Koulich, D., Orlova, M., Malhotra, A., Šali, A., Darst, S. A., and Borukhov, S. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J. Biol. Chem. 272, 7201-7210 (1997).

  23. Hunt, J. E., Friend, D. S., Gurish, M. F., Feyfant, E., Šali, A., Huang, C., Ghildyal, N., Stechshulte, S., Austen, K. F., and Stevens, R. L. Mouse mast cell protease (mMCP) 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells. J. Biol. Chem. 46, 29158-29166 (1997).

  24. Sánchez, R. and Šali, A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins Suppl. 1, 50-58 (1997).

  25. Guenther, B., Onrust, R., Šali, A., O'Donnell, M., and Kuriyan, J. Crystal structure of the $\delta$' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91, 335-345 (1997).

  26. Sánchez, R., Badretdinov, A. Y., Feyfant, E., and Šali, A. Homology protein structure modeling. Transactions Amer. Cryst. Assoc. 32, 81-91 (1997).

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

  28. Huang, C., Šali, A., and Stevens, R. L. Regulation and function of mast cell proteases in inflammation. J. Clin. Immunol. 18, 169-183 (1998).

  29. Kandiah, D. A., Šali, A., Sheng, Y., Victoria, E. J., Marquis, D. M., Coutts, S. M., and Krilis, S. Current insights into the antiphospholipid syndrome: Clinical, immunological and molecular aspects. Adv. Immunol. 70, 507-563 (1998).

  30. Wolf, E., Vassilev, A., Makino, Y., Šali, A., Nakatani, Y., and Burley, S. K. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell 94, 51-61 (1998).

  31. Sánchez, R. and Šali, A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. USA 95, 13597-13602 (1998).

  32. Šali, A. 100,000 protein structures for the biologist. Nat. Struct. Biol. 5, 1029-1032 (1998).

  33. Sánchez, R. and Šali, A. MODBASE : A database of comparative protein structure models. Bioinformatics 15, 1060-1061 (1999).

  34. Fiser, A., Sánchez, R., Melo, F., and Šali, A. Comparative protein structure modeling. In Computational Biochemistry and Biophysics, in press, Watanabe, M., Roux, B., MacKerell, A., and Becker, O., editors. Marcel Dekker (2000).

  35. Sánchez, R. and Šali, A. Comparative protein structure modeling in genomics. J. Comp. Phys. 151, 388-401 (1999).

  36. Wu, G., Fiser, A., ter Kuile, B., Šali, A., and Müller, M. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc. Natl. Acad. Sci. USA 96, 6285-6290 (1999).

  37. Nagata, T., Gupta, V., Kim, W.-Y., Šali, A., Chait, B. T., Shigesada, K., Ito, Y., and Werner, M. H. Immunoglobulin motif DNA recognition and heterodimerization for the PEBP2/CBF Runt-domain. Nat. Str. Biol. 6, 615-619 (1999).

  38. Miwa, J. M., Ibanez-Tallon, I., Crabtree, G. W., Sánchez, R., Šali, A., Role, L. W., and Heintz, N. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. Neuron 23, 105-114 (1999).

  39. Huang, C., Morales, G., Vagi, A., Chanasyk, K., Ferrazzi, M., Burklow, C., Qiu, W. T., Feyfant, E., Šali, A., and Stevens, R. L. Formation of enzymatically active, homotypic and heterotypic tetramers of mouse mast cell tryptases. J. Biol. Chem. 275, 351-358 (2000).

  40. Wong, G. W., Tang, Y., Feyfant, E., Šali, A., Huang, C., and Stevens, R. L. Identification of a new tryptase in mice and humans which possesses a novel C-terminal, membrane spanning segment. J. Biol. Chem. 274, 30784-30793 (1999).

  41. Wu, G., Morrison, H. G., Fiser, A., McArthur, A. G., Šali, A., Sogin, M. L., and Müller, M. Core histones of the amitochondriate protist, Giardia lamblia. Mol. Biol. Evol. 17, 1156-1163 (2000).

  42. Burley, S. K., Almo, S. C., Bonanno, J. B., , Capel, M., Chance, M. R., Gaasterland, T., Lin, D., Šali, A., Studier, F. W., and Swaminathan, S. Structural genomics: beyond the Human Genome Project. Nat. Genet. 23, 151-157 (1999).

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

  44. Sánchez, R., Pieper, U., Mirkovic, N., de Bakker, P. I. W., Wittenstein, E., and Šali, A. MODBASE, a database of annotated comparative protein structure models. Nucl. Acids Res. 28, 250-253 (2000).

  45. Šali, A. and Kuriyan, J. Challenges at the frontiers of structural biology. Trends Biochem. Sci. 22, M20-M24 (1999).

  46. Pieper, U., Eswar, N., Sánchez, R., Mirkovic, N., Lane, W., Sammut, M., John, B., and Šali, A. MODBASE, a database of annotated comparative protein structure models. Nucl. Acids Res. , in press (2001).

  47. Groft, C. M., Beckmann, R., Šali, A., and Burley, S. K. Crystal structures of ribosome anti-association factor IF6. Nat. Struct. Biol. 7, 1156-1164 (2000).

  48. Sánchez, R., Pieper, U., Melo, F., Eswar, N., Martí-Renom, M., Madhusudhan, M., Mirkovic, N., and Šali, A. Protein structure modeling for structural genomics. Nat. Struct. Biol. 7, 986-990 (2000).

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

Please quote A. Šali and T. L. Blundell, ``Comparative protein modelling by satisfaction of spatial restraints'' J. Mol. Biol. 234, 779-815 (1993) in your publications using MODELLER.

I will greatly appreciate it you send me copies of any papers using MODELLER to



Andrej Šali
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry,
and California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240
USA

tel +1 415 514 4227
fax +1 415 514 4231
email sali@salilab.org
URL http://www.salilab.org/

next up previous contents index
Next: Distribution Up: Introduction Previous: What is MODELLER?   Contents   Index
Ben Webb 2004-04-20