Publications

Listed in reverse chronological order.

  1. Peter M. Kasson, Frank DiMaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili, and Edward H Egelman.  Model for a novel membrane envelope in a filamentous hyperthermophilic virus.  Elife 2017.   DOI: 10.7554/eLife.26268.
  2. Malgorzata Latallo, George Cortina, Salem Faham, Robert Nakamoto and Peter M. Kasson.  Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.  Chemical Science, 2017 online July 19.
  3. Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J Russell ,Jessica A Belser, Sarah Cobey, Peter M Kasson, James O Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine AA Beauchemin, Trevor Bedford, Thomas C Friedrich, Andreas Handel, Sander Herfst, Pablo R Murcia, Benjamin Roche, Claus O Wilke, and Colin A Russell.  Viral factors in influenza pandemic risk assessment.  Elife. 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491.
  4. George A. Cortina and Peter M. Kasson.  Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance.  Bioinformatics, 2016 Nov 15;32(22):3420-3427. Epub 2016 Jul 27.
  5. Katarzyna E. Zawada, Dominik Wrona, Robert J. Rawle, and Peter M. Kasson.  Influenza viral membrane fusion is sensitive to sterol concentration but surprisingly robust to sterol chemical identity.  Scientific Reports, 2016 6:29842.
  6. Robert J. Rawle, Steven G. Boxer, and Peter M. Kasson.  Disentangling viral membrane fusion from receptor binding using synthetic DNA-lipid conjugates.  Biophysical Journal, 2016 111: 123-131
  7. Marta Domanska, Rebecca Dunning, Katarzyna Zawada, Kelly Dryden, Mark Yeager, and Peter M. Kasson. Hemagglutinin spatial distribution shifts in response to cholesterol in the influenza viral envelope.  Biophysical Journal, 2015 109 (9) 1917-24
  8. Sander Pronk, Iman Pouya, Magnus Lundborg, Grant Rotskoff, Bjorn Wesen, Peter Kasson, and Erik Lindahl.  Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.  J. Chem. Theory Comput., 2015 11 (6): 2600–2608.
  9. Sander Pronk, Erik Lindahl, and Peter M. Kasson. Coupled diffusion in lipid bilayers upon close approach. Journal of the American Chemical Society. Epub Dec 23, 2014
  10. Michael D. Purdy, Brad C. Bennett, William E. McIntire, Ali Khan, Peter M. Kasson, and Mark Yeager.Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Current Opinion in Structural Biology, 2014 Aug; 27:138-48.
  11. Colin A. Russell, Peter M. Kasson, Ruben O. Donis, Steven Riley, John Dunbar, Andrew Rumbaut, Jason Asher, Stephen Burke, C. Todd Davis, Rebecca J. Garten, S. Gnanakaran, Simon I. Hay, Sander Herfst, Nicola S. Lewis, James O. Lloyd-Smith, Catherine A. Macken, Sebastian Mauerer-Stroh, ElizabethNeuhaus, Colin R. Parris, Kim M. Pepin, Daniel R. Perez, Sam Shepard, David L. Smith, David L. Suarez, Susan C. Trock, Marc-Alain Widdowson, Dylan George, Marc Lipsitch, Jesse D. Bloom. Improving pandemic influenza risk assessment. eLife, 2014 Oct 16; 3:e03883
  12. Per Larsson and Peter M. Kasson. Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations. Journal of Membrane Biology, 2014
  13. Dan A. Fox, Per Larsson, Ryan H. Lo, Brett M. Kroncke, Peter M. Kasson, and Linda Columbus. NMR and MD hybrid approach to the structure ensemble of Opa60: Insights into host interactions that induce phagocytosis. Journal of the American Chemical Society, 2014. Epub May 9.
  14. Sonia M. Gregory, Per Larsson, Elizabeth A. Nelson, Peter M. Kasson, Judith M. White, and Lukas K. Tamm.Ebolavirus entry requires a compact hydrophobic fist at the tip of the fusion loop. Journal of Virology, 2014. 88:12 6636-6649.
  15. Sander Pronk, Erik Lindahl, and Peter M. Kasson.  Dynamic heterogeneity controls diffusion and viscosity near biological interfaces.  Nature Communications, 2014 Jan 8; 5:3034.
  16. Marta K. Domanska, Dominik Wrona, and Peter M. Kasson.  Multiphasic effects of cholesterol on influenza fusion kinetics reflect multiple mechanistic roles.  Biophysical Journal, 2013 Sept 17; 105(6).
  17. Per Larsson and Peter M. Kasson.  Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models.  PLoS Computational Biology.  2013 March 7 9(3): e1002950.
  18. Sander Pronk, Szillard Pall, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, and Erik Lindahl.  GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit.  Bioinformatics.  2013.  Epub 2013 Feb 13.
  19. Peter M. Kasson*, Berk Hess, and Erik Lindahl*.  Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions.  Chemistry and Physics of Lipids.  2013. Epub 2013 Jan 12.
  20. Peter M. Kasson.  Receptor binding by influenza virus:  using computational techniques to extend structural data.  Biochemistry.  2012 Mar 27; 51(12): 2359-65.
  21. Sander Pronk, Per Larsson, Iman Pouya, Gregory Bowman, Imran Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande*, Peter M. Kasson*, and Erik Lindahl*.  Copernicus: a new paradigm for parallel adaptive molecular dynamics. Supercomputing 2011.
  22. Peter M. Kasson and Vijay S. Pande.  A bundling of viral fusion mechanisms.  Proceedings of the National Academy of Sciences.  2011 Feb 28.
  23. Peter M. Kasson, Erik Lindahl, and Vijay S. Pande.  Water ordering at membrane interfaces controls fusion dynamics.  J Am Chem Soc. 2011; 133(11):3812-15.
  24. Peter M. Kasson, Erik Lindahl, and Vijay S. Pande. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.  PLoS Computational Biology, 2010 June 24; 6(6)e1000829.
  25. Peter M. Kasson and Vijay S. Pande.  “Cross-graining.”  Efficient multi-scale simulation via Markov State Models.  Pacific Symposium on Biocomputing.  2010:260-8.
  26. Peter M. Kasson, Daniel L. Ensign, and Vijay S. Pande.  Combining molecular dynamics with Bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.  J Am Chem Soc. 2009 Aug 19;131(32):11338-40.  Epub 2009 July 28.
  27. Peter M. Kasson and Vijay S. Pande.  Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin.  Pac Symp Biocomput. 2009:492-503.
  28. Peter M. Kasson and Vijay S. Pande.  Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin.  Biophys J. 2008 Oct;95(7):L48-50.  Epub 2008 July 18.
  29. Peter M. Kasson and Vijay S. Pande.  Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics.  PLoS Computational Biology, 2007 Nov; 3(11)e220.  Epub 2007 Sept 26.
  30. Daniel L. Ensign, Peter M. Kasson, and Vijay S. Pande.  Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.  J. Mol. Biol., 2007 Nov 30; 374(3):806-16.  Epub 2007 Oct 1.
  31. Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, and Vijay S. Pande. Persistent voids:  a new structural metric for membrane fusion.  Bioinformatics. 2007 Jul 15;23(14):1753-9. Epub 2007 May 8.
  32. Peter M. Kasson and Vijay S. Pande.  Predicting structure and dynamics of loosely-ordered protein complexes:  influenza hemagglutinin peptide.  Pacific Symposium on Biocomputing. 2007 12:40-50.
  33. Peter M. Kasson, Nicholas W. Kelley, Nina Singhal, Marija Vrljic, Axel T. Brunger, and Vijay S. Pande. Ensemble molecular dynamics yields sub-millisecond kinetics and intermediates of membrane fusion.  Proceedings of the National Academy of Sciences. 2006 Aug 8;103(32):11916-21. Epub 2006 Jul 31.
  34. Peter M. Kasson, Johannes B. Huppa, Mark M. Davis, and Axel T. Brunger.  A hybrid machine-learning approach for segmentation of protein localization data.  Bioinformatics. 2005 Oct 1;21(19):3778-86. Epub 2005 Aug 9.
  35. Peter M. Kasson, Mark M. Davis, and Axel T. Brunger.  Deformable modeling for improved calculation of molecular velocities from single-particle tracking.  2005 EEE Computational Systems Bioinformatics Conference 8-11 Aug. 2005.
  36. Peter M. Kasson, Johannes B. Huppa, Michelle Krogsgaard, Mark M. Davis, and Axel T. Brunger. Quantitative imaging of lymphocyte membrane protein reorganization and signaling.  Biophys J. 2005 Jan;88(1):579-89.
  37. Peter M. Kasson, Johannes B. Huppa, Mark M. Davis, and Axel T. Brunger.  Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy.  Proceedings – International Conference on Image Processing.  2004; v.2, p.2933-2936.
  38. Peter M. Kasson and Vijay S. Pande.  Molecular dynamics simulation of lipid reorientation at bilayer edges.  Biophys J. 2004 Jun;86(6):3744-9.
  39. Peter M. Kasson, Joshua D. Rabinowitz, Lutz Schmitt, Mark M. Davis, and Harden M. McConnell.  Kinetics of Peptide Binding to the class II MHC protein I-Ek.  Biochemistry, 2000 Feb 8;39(5):1048-58.
  40. Joshua D. Rabinowitz, Maria Vrljic, Peter M. Kasson, Michael N. Liang, Robert Busch, J.J Boniface, Mark M. Davis, and Harden M. McConnell.  Formation of a Highly Peptide-Receptive State of Class II MHC.  Immunity, 1998 Nov;9(5):699-709.