Michel Frédéric SANNER

Panels and Reviews:
Co-organizer of the SciPy'02 workshop, September 5-6, 2002, CalTech, Pasadena, CA.
Member of the study section ZRG1 SSSH (90) Computational Biology, since October 2002.
Reviewer for the Bioinformatics mini track at the 36th Hawaii International Conference on System Sciences. 2002
Reviewer for the Pacific Symposium on Biocomputing (PSB) 2000.
Reviewer for the IEEE Viz03.
Reviewer for Protein Engineering
Reviewer for Journal of Computational Chemistry
Reviewer for Bioinformatics
Reviewer for Journal of Molecular Graphics and Modelling
Reviewer for Structure
Reviewer for Encyclopedia of Life Sciences, John Wiley & Sons
Reviewer for Addison-Wesley
Consultation:
Scientific Consultant, Pfizer, 2000-2001
Memberships:
Molecular Graphics and Modeling Society
ACM
Invited talks:
AMI forum. Component-Based Software Development, Applications to Structural Molecular Biology. Jan. 16, 2003
Lecture at the Paris research center of Aventis Pharma, Department of structural biology. August 19th 2002.
Gordon conference, Diffraction methods, New London, July 2002
IUCr, Geneva, August 2002
Gordon conference, Diffraction methods, New London, July 2002
Distinguished TICAM Faculty fellow from 2/7/2002 to 2/24/2002. Texas Institute of Applied Mathematics.
UCSF, Computer Graphics Laboratory, 1999
UCSD, Technical exchange seminar (TEA) August 1999
Tutorials taught:,
Sophie Coon and Michel Sanner. NPACI Visualization Packages: The Python Molecular Viewer and its components. Taught at the NPACI AllHands meeting, March 6 2002. San Diego.
Sophie Coon and Michel Sanner. NPACI Visualization Packages: The Python Molecular Viewer and its components. Taught at the NPACI AllHands meeting, February 25 2001. San Diego.
Sophie Coon and Michel Sanner. Python for Structural Bioinformatics.. Taught at the NPACI AllHands meeting, March 18 2003. San Diego.
Sophie Coon and Michel Sanner. Python for Structural Bioinformatics. Taught at the Pacific Symposium on Biocomputing (PSB) 2001.

1. Michel Sanner, Armin Widmer, Hans Senn and Werner Braun (1989). GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data. Journal of Computer Aided Molecular Design, 3, 195-210.
2. Hans Senn, Hans-Rudolf Loosli, Michel Sanner and Werner Braun (1990). Conformational Studies of Cyclic Peptide Structures in Solution from 1H-Nmr Data by Distance Geometry Calculation and Restrained Energy Minimization. Biopolymers, Vol. 29, 1387-1400.


3. Michel Sanner and Jean Claude Spehner (1992). Geometrical decomposition of Connolly surfaces. Internal publication of the University of Haute-Alsace. Modelling and Computational Geometry Laboratory, FST, 4 rue des Frères Lumière 68093 Mulhouse, France.
4. Michel Sanner, Arthur J. Olson, Jean Claude Spehner (1995). Fast and Robust Computation of Molecular Surfaces. Proc. 11th ACM Symp. Comp. Geom, C6-C7.
5. Michel Sanner, Arthur J. Olson, Jean Claude Spehner (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers, Vol 38, (3), 305-320.
Full paper (acrobat 537K).
6. Boris A. Reva, Michel F. Sanner, Arthur J. Olson, Alexei V. Finkelstein (1995). Lattice modelling: accuracy of energy calculations. Journal of Computational Chemistry. Vol 17, No 8, 1025-1032.
7. Michel F. Sanner, Boris A. Reva, Alexei V. Finkelstein and Arthur J. olson. (1996). Increasing accuracy of energy calculations of lattice models by adjusting the potentials. Proc. First Pacific Symposium in Biocomputing.
8. Boris A. Reva, Alexei V. Finkelstein, Michel F. Sanner and Arthur J. Olson, (1996). Adjusting potential energy functions for lattice models of chain molecules. Proteins, Structures, Function, and Genetics. 25:379-388.
9. Michel F. Sanner and Arthur J. olson. (1997) Real Time Surface Reconstruction For moving Molecular Fragments. Proc. Second Pacific Symposium in Biocomputing.
   Full paper (acrobat 79K).
10. Reva, B. A., Finkelstein, A. V., Sanner, M. F. and Olson, A. J. (1997). Accurate Mean-Force Pairwise-Residue Potentials for Discrimination of Protein Folds. Proc. Second Pacific Symposium in Biocomputing.
    Full paper (acrobat 57K).
11. J. Schroer, M. F. Sanner, J.L. Reymond and R.A. Lerner. (1997). Design and synthesis of transition state analog for induction of hydride transfer catalytic antibodies. Journal of Organic Chemistry. Vol. 62, Number 10, 3220-3229.
12. Reva, B. A., Finkelstein, A. V., Sanner, M. F. and Olson, A. J. (1997). Residue-residue mean force potentials for protein structure recognition. Protein Engineering. Vol 10, no. 8, 865-876.
    Full paper (acrobat 57K).
13. Reva, B. A., Finkelstein, A. V., Sanner, M. F., Olson, A. J. and Skolnick J. (1997). Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein Engineering. Vol 10. no. 10, 1123-1130.
    Full paper (acrobat 57K).
14. Michel F. Sanner, Bruce S. Duncan, Christian J. Carrillo and Arthur J. Olson. (1998). Integrating Computation and Visualization for Biomolecular Analysis: An example using Python and AVS. Proc. Pacific Symposium in Biocomputing `99. pp 401-412.
    Full paper (acrobat 104K).
15. Burkhard, P., Hommel, U., Sanner, M., and Walkinshaw, M. D.(1998). The discovery of steroids and other novel FKBP inhibitors using a molecular docking program. J. Mol. Biol. 287(5):853-8, 1999 Apr 16.
    Full paper (acrobat 79K).
16. Michel F. Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod., 1999, Vol 17, February. pp 57-61.
    Full paper (acrobat 326K).
17. Sophie I. Coon, Michel F. Sanner and Arthur J. Olson. Re-Usable components for Structural Bioinformatics. In Proceedings of the 9th International Python conference. pp 157-166, March 5-8, 2001. Long Beach, California.
    Full paper (acrobat 221K).
18. Osterberg, F., Morris, G.M., Sanner, M.F., Olson A.J., and Goodsell, D.S. Automated Docking to multiple Target Structures: Incorporation of Protein Mobility and Structural Water Heterogeneity in AutoDock. PROTEINS: Structure, Function, and Genetics 46:34-40. (2002).
    Full paper (acrobat 455K).
19. Glen B. Legge, Garrett M. Morris, Michel F. Sanner, Yoshikazu Takada, Arthur J. Olson, and Flavio Grynszpan (2002). Model of the alpha L beta 2 Integrin I-Domain/ICAM-1 DI Interface Suggests That Subtle Changes in Loop Orientation Determine Ligand Specificity. PROTEINS: Structure, Function, and Genetics 48:151-160.
    Full paper (acrobat 2.1Mb).
20. Sanner M.F., Stoffler D. and Olson A.J. (2002). ViPEr, a visual Programming Environment for Python. In Proceedings of the 10th International Python conference. 103-115. February 4-7, 2002. ISBN 1-930792-05-0.
    Full paper (acrobat 2.4Mb).
21. Daniel Stoffler, Michel F. Sanner, Garrett M. Morris, Arthur J. Olson, David S. Goodsell. Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance. PROTEINS: Structure, Function, and Genetics 48:63-74 (2002).
    Full paper (acrobat 2.4Mb).
22. Michel F. Sanner. Component-based Software Development, Applications to Structural Biology.. Acta Cryst. A58 (supplement)C218 (2002).
    
23. Daniel Stoffler, Sophie I. Coon, Ruth Huey, Arthur J. Olson and Michel F. Sanner. Integrating Biomolecular Analysis and Visual Programming: Flexibility and Interactivity in the Design of Bioinformatics Tools. Proceedings of the Thirty-Sixth Annual Hawaii International Conference on System Sciences (CD/ROM), January 6-9, 2003, Computer Society Press, 2003. Ten pages.
    HICSS digital library. or Full paper (acrobat 4.7Mb).
24. Ganesh Sankaranarayana, Suzanne Weghorst, Michel F. Sanner, Alexandre Gillet Arthur J. Olson. Role of Haptics in Teaching structural Molecular Biology. In proceedings of 11th international Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, March 22-23 2003 Los Angels Ca. IEEE committee on Visualization and Graphics. pp. 363-266. ISBN 0-7695-1890-7.
25. Alexandre Gillet, David Goodsell, Michel Sanner, Daniel Stoffler, Suzanne Weghorst, William Winn and Arthur Olson. Computer-Linked Autofabricated 3D Model For Teaching Structural Biology. In Proceeding of Siggraph 2004.
26. Alexandre Gillet, David Goodsell, Michel Sanner, Daniel Stoffler and Arthur Olson. A Tangible Model Augmented Reality Aplication for Molecular Biology. in Proceeding of IEEE Visualization 2004, p235-241.
27. Alexandre Gillet, Michel Sanner, Daniel Stoffler and Arthur Olson. Tangible Augmented Interfaces for Structural Molecular Biology. IEEE Computer Graphics and Applications. March-April 2005, Vol 25, Number 2, p13-17.
28. Michel Sanner A Component-Based Software Environment for Visualizing Large Macromolecular Assemblies. Structure, Vol 13, 447-462, March 2005. Full paper.
29. Alexandre Gillet, Michel Sanner, Daniel Stoffler and Arthur Olson Tangible Interfaces for Structural Molecular Biology. Structure, Vol 13, 483-491, March 2005. Full paper.
30. Michel F. Sanner, Martin Stolz, Peter Burkhard, Xiang-Peng Kong, Guangwei Min, Tung-Tien Sun, Sergey Driamov, Ueli Aebi, and Daniel Stoffler. Visualizing Nature at Work from the Nano to the Macro Scale. NanoBiotechnology, Volume 1, 2005, Proteomics and Bioinformatics. John Wiley & sons, Ltd. (2005). pp7-11. ISSN 1551-1286/05/01:7 22/$30.00 DOI: 10.1385/Nano:1:1:7 Full paper PDF.
31. Wilfred W. Li, Sriram Krishnan, Kurt Mueller, Kohei Ichikawa, Susumu Date, Sartgis Dallakyan, Michel F. Sanner, Chris Misleh, Zhaohui Ding, Xiaohui Wei, Osamu Tatebe, Peter W. Arzberger. Building Cyberinfrastructure for Bioinformatics Using Serce Oriented Architecture in proceeding of 6th IEEE International Symposium on Cluster Computing and the Grid. Singapore May-16-19.
32. Wilfred W. Li, Nathan Baker, Kim Baldrige, J. Andrew McCammon, Mark H. Ellisman, Amarnath Gupta,Michael Holst, Andrew McCulloch, Anushka Michailova, Phil Papadopoulos, Art Olson, Michel Sanner, Peter Arzterbger. national Biomedical Computation resource (nBCr): Developing End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research CTWatch Quarterly August 2006. pp6-17.
33. Yong Zhao, Daniel Stoffler and Michel Sanner.Hierarchical and multi-resolution representation of protein flexibility BIOINFORMATICS, Structural bioinformatics, Vol. 22, no. 22, 2006, pages 2768-2774. Full paper PDF (subscription to Bioinformatics required).Email me for a pdf [sanner at scripps.edu]
34. Yong Zhao and Michel Sanner. FLIPDock: Docking Flexible Ligands into Flexible Receptors Proteins: Structure, Function, and Bioinformatics. 2007, 68, (3), 726-737.
35. Lorenzo Bongini, Duccio Fanelli, Francesco Piazza, Paolo De Los Rios, Michel Sanner and Ulf Skoglund. A dynamical study of antibody-antigen encounter reactions. Physical Biology, Volume 4, Number 3, September 2007, pp172-180. doi:10.1088/1478-3975/4/3/004. Available online
36. Yong Zhao and Michel F. Sanner. Protein-ligand docking with multiple flexible side chains Journal of Computer-Aided Molecular Design. 2007. http://dx.doi.org/10.1007/s10822-007-9148-5

TALKS

1. Python and tools inter-operability:
An application in bio-computing  Michel F. SANNER  Molecular Graphics and Computation Laboratory, The Scripps Research Institute  PostScript Overheads of the presentation. Python is a very high level, interpreted, object-oriented language that was released first in 1990. It has an eclectic design taking ideas from several programing languages such as ABC, C, C++, Modula-3 and others. Along with the dynamic scripting capability provided by interpreted languages such as Tcl and Perl it offers features from general programing languages. It is therefore a tool of choice for developments ranging from "use once" scripts to full fledge applications.

 The language can easily be extended with new functions and objects implemented in Python but also in C or C++ whenever utmost efficiency is required. Moreover, it is straight forward to embed a Python interpreter into a C or C++ program. These are key features for using Python as a simple, and yet powerful, programmable environment in which different tools can share and operate on sets of data.

 After a brief introduction to the Python programing language and a short description of Numeric Python - an extension module that enable the efficient handling of large arrays of data - several examples will be presented that illustrate both:

 extending Python with new objects and functions such as:

 

• - reading Brookhaven Protein Data Base (PDB) files
• - computing molecular surfaces (MSMS)
• - performing molecular mechanics/dynamics calculations (Amber)
• - performing docking calculations (AutoDock, SurfDock)

 and embedding a Python interpreter into other packages like:

 

• - AVS: the interpreter is embedded in an AVS module adding 3D graphics capability to the interpreter, and enabling efficient, Python-script based, module development.
• - MSV: a molecular surface viewer.

 

Examples will illustrate how these different components inter-operate within a Python interpreter by sharing objects and data.