CCL: Homology modeling and loop refinement

 Sent to CCL by: Shikha Varma [SVarma%x%accelrys.com]
 Dear Werner,
 You can try MODELER for homology modeling and CHARMm based algorithm Looper for
 loop refinement.  Both methods are implemented in Accelrys Discovery Studio
 modeling package.
 MODELER program is developed by Andrej Sali (http://salilab.org/index.html) and is the best homology
 modeling package available.  It is used as the official model building program
 by CASP (http://predictioncenter.org/index.cgi), a community
 organized Critical Assessment of techniques for protein Structure Prediction.
 It is highly automated and has many unique features, such as allowing you to
 create model including ligands, build multiple chain protein with symmetry
 constraints, etc, to make the model building easy and accurate.
 Looper (Spassov, V.Z., et al, Protein Engineering Design and Selection 2008,
 21(2), 91-100) is an algorithm developed at Accelrys and is a very fast and
 accurate loop prediction method.  It is based on the well known CHARMm (CHARMM)
 simulation engine developed at Harvard university. The implementation of LOOPER
 algorithm in  Loop Refinement protocol is based on  CHARMm energy calculations
 and it is flexible to  a choice of most of  CHARMm forcefields what allows the
 predicted structures to be used directly by other modeling protocols, such as MD
 simulations, pK predictions etc.
 Publications of interest:
 1. Spassov, V. Z.; Yan, L. A fast and accurate computational approach to protein
 ionization. Protein Sci. 2008, 17, 1955-1970.
 2.Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P. K.;
 Venkatachalam, C. M. Fully automated molecular mechanics based induced fit
 protein-ligand docking method. J. Chem. Inf. Model. 2008, 48, 1965-1973.
 3. Eswar, N.; Eramian, D.; Webb, B.; Shen, M. Y.; Sali, A. Protein structure
 modeling with MODELLER. Methods Mol. Biol. 2008, 426, 145-159.
 4. Spassov, V.; Yan, L.; Flook, P. The dominant role of side-chain backbone
 interactions in structural realization of amino acid code. ChiRotor: a
 side-chain prediction algorithm based on side-chain backbone interactions.
 Protein Sci. 2007, 16, 494-506.
 5. Marti-Renom, M. A.; Madhusudhan, M. S.; Sali, A. Alignment of protein
 sequences by their profiles. Protein Sci. 2004, 13, 1071-1087.
 6. Li, L.; Chen, R.; Weng, Z. RDOCK: refinement of rigid-body protein docking
 predictions. Proteins 2003, 53, 693-707.
 Chen, R.; Li, L.; Weng, Z. ZDOCK: an initial-stage protein-docking algorithm.
 Proteins 2003, 52, 80-87.
 Morea, V.; Lesk, A.; Tramontano, A. Antibody modeling: implications for
 engineering and design. Methods 2000, 20, 267-279.
 7. Sali, A.; Pottertone, L.; Yuan, F.; van Vlijmen, H.; Karplus, M.; Evaluation
 of comparative protein modeling by MODELLER. Proteins 1995, 23, 318-326.
 8. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen,
 U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER.
 Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15,
 5.6.1-5.6.30, 2006.
 9. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali.
 Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys.
 Biomol. Struct. 29, 291-325, 2000.
 A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of
 spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
 10. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures,
 Protein Science 9. 1753-1773, 2000.
 Shikha Varma-O'Brien, Ph.D.
 Director, LS Modeling & Simulations
 Accelrys, Inc.
 10188 Telesis Court, Suite 100
 San Diego, CA 92121, USA
 Ph: +1 858 799 5607
 Fax: +1 858 799 5100
 Stay Connected with Accelrys and the
 Scientific & Engineering Community
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 -----Original Message-----
 > From: owner-chemistry+shikha==accelrys.com_._ccl.net [mailto:owner-chemistry+shikha==accelrys.com_._ccl.net] On Behalf Of Werner
 K werner.schroedinger-x-googlemail.com
 Sent: Wednesday, November 04, 2009 8:53 AM
 To: Shikha Varma
 Subject: CCL: Homology modeling and loop refinement
 Sent to CCL by: "Werner  K" [werner.schroedinger^-^googlemail.com]
 Hi,
 what are in your opinion the best softwares, free and commercial, for protein
 homology modeling and loop refinement?
 Thanks
 WS
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