recent publications
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academic article
- 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
- 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
- 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
- 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
- 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. F., Olson, A. J. Accurate mean-force pairwise-residue potentials for discrimination of protein folds Pacific Symposium on Biocomputing 1997 373-384 PMID:9390307
- 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
- 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., 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
- 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
- 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
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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
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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