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Sanner, Michel
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Sanner, Michel

Faculty Member
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Positions

  • 2013 - Associate Professor of Molecular Biology, Integrative Structural and Computational Biology (ISCB) , Scripps Research
  • 2004 - 2012 Associate Professor of Molecular Biology, Molecular Biology , Scripps Research
  • 1998 - 2004 Assistant Professor, Molecular Biology , Scripps Research

Dr. Michel Sanner has pioneered a strategy for developing interoperable software components for the visualization and modelling of biomolecular interactions resulting in various software tools widely used by scientist in the field of computational structural biology, including MSMS: a software program for computing molecular surfaces; Software tools for the visualization and manipulation of molecules: PMV and AutoDockTools, and docking engines such as AutoDock4 (small molecule docking), AutoDockFR (Flexible Receptor) and AutoDock CrankPep (peptide docking). 

Contact

  • sanner@scripps.edu

Websites

  • Michel Sanner, Ph.D.
  • Sanner Laboratory
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Publications

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  • Publications without PubMed PMIDs

  • academic article

    • Yamashita, A., Zhang, Y. Q., Sanner, M. F., Griffin, J. H., Mosnier, L. O. C-terminal residues of activated protein C light chain contribute to its anticoagulant and cytoprotective activities Journal of Thrombosis and Haemostasis  2020 18:1027-1038  DOI:10.1111/jth.14756  PMID:32017367
    • Goodsell, D. S., Sanner, M. F., Olson, A. J., Forli, S. The AutoDock suite at 30 Protein Science  2020  DOI:10.1002/pro.3934  PMID:32808340
    • Zhang, Y., Sanner, M. F. AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes Bioinformatics  2019 35:5121-5127  DOI:10.1093/bioinformatics/btz459  PMID:31161213  PMCID:PMC6954657
    • Zhang, Y., Forli, S., Omelchenko, A., Sanner, M. F. AutoGridFR: Improvements on AutoDock affinity maps and associated software tools Journal of Computational Chemistry  2019  DOI:10.1002/jcc.26054  PMID:31436329
    • Zhang, Y., Sanner, M. F. Docking flexible cyclic peptides with AutoDock CrankPep Journal of Chemical Theory and Computation  2019 15:5161-5168  DOI:10.1021/acs.jctc.9b00557  PMID:31505931
    • Fernandez, J. A., Xu, X., Sinha, R. K., Mosnier, L. O., Sanner, M. F., Griffin, J. H. Activated protein C light chain provides an extended binding surface for its anticoagulant cofactor, protein S Blood Advances  2017 1:1423-1426  DOI:10.1182/bloodadvances.2017007005  PMID:29296783  PMCID:PMC5727852
    • Ravindranath, P. A., Sanner, M. F. AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms Bioinformatics  2016 32:3142-3149  DOI:10.1093/bioinformatics/btw367  PMID:27354702  PMCID:PMC5048065
    • Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., Olson, A. J. Computational protein-ligand docking and virtual drug screening with the AutoDock suite Nature Protocols  2016 11:905-919  DOI:10.1038/nprot.2016.051  PMID:27077332  PMCID:PMC4868550
    • Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., Sanner, M. F. AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility PLoS Computational Biology  2015 11  DOI:10.1371/journal.pcbi.1004586  PMID:26629955  PMCID:PMC4667975
    • Johnson, G. T., Autin, L., Al-Alusi, M., Goodsell, D. S., Sanner, M. F., Olson, A. J. cellPACK: a virtual mesoscope to model and visualize structural systems biology Nature Methods  2015 12:85-91  DOI:10.1038/nmeth.3204  PMID:25437435  PMCID:PMC4281296
    • Johnson, G. T., Goodsell, D. S., Autin, L., Sanner, M. F., Olson, A. J. 3D molecular models of whole HIV-1 virions generated with cellPACK Faraday Discussions  2014 169:23-44  DOI:10.1039/c4fd00017j  PMID:25253262  PMCID:PMC4569901
    • Chowdhury, R., Rasheed, M., Keidel, D., Moussalem, M., Olson, A., Sanner, M., Bajaj, C. Protein-protein docking with F(2)Dock 2.0 and GB-rerank PLoS One  2013 8:e51307  DOI:10.1371/journal.pone.0051307  PMID:23483883  PMCID:PMC3590208
    • Autin, L., Johnson, G., Hake, J., Olson, A., Sanner, M. uPy: a ubiquitous CG Python API with biological-modeling applications IEEE Computer Graphics and Applications  2012 32:50-61  DOI:10.1109/MCG.2012.93  PMID:24806987  PMCID:PMC4590990
    • Johnson, G. T., Olson, A. J., Sanner, M. F., Goodsell, D. S., Autin, L. ePMV embeds molecular modeling into professional animation software environments Structure  2011 19:293-303  DOI:10.1016/j.str.2010.12.023  PMID:21397181  PMCID:PMC3101797
    • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., Olson, A. J. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility Journal of Computational Chemistry  2009 30:2785-2791  DOI:10.1002/jcc.21256  PMID:19399780  PMCID:PMC2760638
    • Dawson, M. I., Ye, M., Cao, X. H., Farhana, L., Hu, Q. Y., Zhao, Y., Xu, L. P., Kiselyuk, A., Correa, R. G., Yang, L., Hou, T. J., Reed, J. C., et al. Derivation of a retinoid x receptor scaffold from peroxisome proliferator-activated receptor gamma ligand 1-di(1h-indol-3-yl)methyl-4-trifluoromethylbenzene ChemMedChem  2009 4:1106-1119  DOI:10.1002/cmdc.200800447  PMID:19378296  PMCID:PMC3031428
    • Zhang, Q., Sanner, M., Olson, A. J. Shape complementarity of protein-protein complexes at multiple resolutions Proteins-Structure Function and Bioinformatics  2009 75:453-467  DOI:10.1002/prot.22256  PMID:18837463  PMCID:PMC2928789
    • Zhao, Y., Sanner, M. F. Protein-ligand docking with multiple flexible side chains Journal of Computer-Aided Molecular Design  2008 22:673-679  DOI:10.1007/s10822-007-9148-5  PMID:18034309  PMCID:PMC4828239
    • Bongini, L., Fanelli, D., Piazza, F., De Los Rios, P., Sanner, M., Skoglund, U. A dynamical study of antibody-antigen encounter reactions Physical Biology  2007 4:172-180  DOI:10.1088/1478-3975/4/3/004  PMID:17928656
    • Zhao, Y., Sanner, M. F. Flipdock: Docking flexible ligands into flexible receptors Proteins-Structure Function and Bioinformatics  2007 68:726-737  DOI:10.1002/prot.21423  PMID:17523154
    • Zhao, Y., Stoffler, D., Sanner, M. Hierarchical and multi-resolution representation of protein flexibility Bioinformatics  2006 22:2768-2774  DOI:10.1093/bioinformatics/btl481  PMID:16984893
    • Sanner, M. F. A component-based software environment for visualizing large macromolecular assemblies Structure  2005 13:447-462  DOI:10.1016/j.str.2005.01.010  PMID:15766546
    • Gillet, A., Sanner, M., Stoffler, D., Olson, A. Tangible augmented structural molecular interfaces for biology IEEE Computer Graphics and Applications  2005 25:13-17  DOI:10.1109/mcg.2005.47  PMID:15794144
    • Gillet, A., Sanner, M., Stoffler, D., Olson, A. Tangible interfaces for structural molecular biology Structure  2005 13:483-491  DOI:10.1016/j.str.2005.01.009  PMID:15766549
    • Legge, G. B., Morris, G. M., Sanner, M. F., Takada, Y., Olson, A. J., Grynszpan, F. 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  2002 48:151-160  DOI:10.1002/prot.10134  PMID:12112684
    • Stoffler, D., Sanner, M. F., Morris, G. M., Olson, A. J., Goodsell, D. S. Evolutionary analysis of HIV-1 protease inhibitors: methods for design of inhibitors that evade resistance Proteins-Structure Function and Genetics  2002 48:63-74  DOI:10.1002/prot.10130  PMID:12012338
    • Osterberg, F., Morris, G. M., Sanner, M. F., Olson, A. J., Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock Proteins-Structure Function and Genetics  2002 46:34-40  DOI:10.1002/prot.10028  PMID:11746701
    • Sanner, M. F., Duncan, B. S., Carrillo, C. J., Olson, A. J. Integrating computation and visualization for biomolecular analysis: an example using Python and AVS Pacific Symposium on Biocomputing  1999 401-412  PMID:10380214
    • Reva, B. A., Finkelstein, A. V., Sanner, M., Olson, A. J., Skolnick, J. Recognition of protein structure on coarse lattices with residue-residue energy functions Protein Engineering  1997 10:1123-1130  DOI:10.1093/protein/10.10.1123  PMID:9488137
    • Sanner, M. F., Olson, A. J. Real time surface reconstruction for moving molecular fragments Pacific Symposium on Biocomputing  1997 385-396  PMID:9390308
    • Reva, B. A., Finkelstein, A. V., Sanner, M. F., Olson, A. J. Residue-residue mean-force potentials for protein structure recognition Protein Engineering  1997 10:865-876  DOI:10.1093/protein/10.8.865  PMID:9415437
    • Schroer, J., Sanner, M., Reymond, J. L., Lerner, R. A. Design and synthesis of transition state analogs for induction of hydride transfer catalytic antibodies Journal of Organic Chemistry  1997 62:3220-3229  DOI:10.1021/jo962179v  PMID:11671707
    • Reva, B. A., Finkelstein, A. V., Sanner, M. F., Olson, A. J. Accurate mean-force pairwise-residue potentials for discrimination of protein folds Pacific Symposium on Biocomputing  1997 373-384  PMID:9390307
    • Reva, B. A., Finkelstein, A. V., Sanner, M. F., Olson, A. J. Adjusting potential energy functions for lattice models of chain molecules Proteins-Structure Function and Genetics  1996 25:379-388  DOI:10.1002/(sici)1097-0134(199607)25:3<379::aid-prot9>3.0.co;2-a  PMID:8844872
    • Reva, B. A., Sanner, M. F., Olson, A. J., Finkelstein, A. V. Lattice modeling: accuracy of energy calculations Journal of Computational Chemistry  1996 17:1025-1032  DOI:10.1002/(sici)1096-987x(199606)17:8<1025::aid-jcc11>3.0.co;2-d
    • Sanner, M. F., Olson, A. J., Spehner, J. C. Reduced surface: an efficient way to compute molecular surfaces Biopolymers  1996 38:305-320  DOI:10.1002/(sici)1097-0282(199603)38:3<305::aid-bip4>3.0.co;2-y  PMID:8906967
    • Papoian, R., Duffy, F., Sanner, M., Wilt, E. A sensitive elisa for measuring recombinant human interleukin-3 in human plasma or serum Journal of Immunological Methods  1991 145:161-165  DOI:10.1016/0022-1759(91)90322-7  PMID:1765647
    • Senn, H., Loosli, H. R., Sanner, M., Braun, W. Conformational studies of cyclic peptide structures in solution from h-1-NMR data by distance geometry calculation and restrained energy minimization Biopolymers  1990 29:1387-1400  DOI:10.1002/bip.360291006  PMID:2361151
    • Sanner, M., Widmer, A., Senn, H., Braun, W. Geom - a new tool for molecular modeling based on distance geometry calculations with NMR data Journal of Computer-Aided Molecular Design  1989 3:195-210  DOI:10.1007/bf01533068  PMID:2585001
  • book

    • Gillet, A., Weghorst, S., Winn, W., Stoffler, D., Sanner, M., Goodsell, D., Olson, A. Computer-linked autofabricated 3D models for teaching structural biology International Conference on Computer Graphics and Interactive Techniques ACM, 2 Penn Plaza, Suite 701, New York, NY 10121-0701, USA. 2004
  • chapter

    • Gillet, A., Sanner, M., Stoffler, D., Goodsell, D., Olson, A. Augmented reality with tangible auto-fabricated models for molecular biology applications IEEE Visualization 2004. 235-241. 2004  DOI:10.1109/VISUAL.2004.7

featured in

  • Touching Molecules With Your Bare Hands: Scripps Research Scientists Describe New Way of Interacting with the Unseen World of Proteins and DNA  News Release
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Research

research overview

  • Molecular interactions, molecular graphics, component-based software

    Work in our laboratory is producing versatile components that can be assembled rapidly to produce custom applications for analyzing macromolecular structures and simulate their interactions. We have released several tools to the scientific community including PMV a general purpose molecular visualization environment, AutoDockTools (ADT) a front end to the automated docking program AutoDock and ViPEr, a visual programming environment in which a user can drag-and-drop computational nodes and connect them to create interactively computational pipelines that combine various computational methods in new ways without having to write code.
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Background

education and training

  • Ph.D. in Biology, University of Haute-Alsace
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Contact

full name

  • Michel F. Sanner

geographic location

  • Scripps California 

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