Peter M. Kasson


  • MD/PhD, Stanford University


Research Interest(s)

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Selected Publications

  • Domanska M, Dunning R, Dryden K, Zawada K, Yeager M, Kasson P. Hemagglutinin Spatial Distribution Shifts in Response to Cholesterol in the Influenza Viral Envelope. Biophysical journal. 2015;109(9): 1917-24. PMID: 26536268
  • Pronk S, Pouya I, Lundborg M, Rotskoff G, Wesén B, Kasson P, Lindahl E. Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform. Journal of chemical theory and computation. 2015;11(6): 2600-8. PMID: 26575558
  • Fox D, Larsson P, Lo R, Kroncke B, Kasson P, Columbus L. Structure of the neisserial outer membrane protein opa60: loop flexibility essential to receptor recognition and bacterial engulfment. Journal of the American Chemical Society. 2014;136(28): 9938-46. PMID: 24813921 | PMCID: PMC4105060
  • Gregory S, Larsson P, Nelson E, Kasson P, White J, Tamm L. Ebolavirus Entry Requires a Compact Hydrophobic Fist at the Tip of the Fusion Loop. Journal of virology. 2014. PMID: 24696482 | PMCID: PMC4054381
  • Larsson P, Kasson P. Lipid Converter, A Framework for Lipid Manipulations in Molecular Dynamics Simulations. The Journal of membrane biology. 2014. PMID: 25081234
  • Pronk S, Lindahl E, Kasson P. Coupled diffusion in lipid bilayers upon close approach. Journal of the American Chemical Society. 2014;137(2): 708-14. PMID: 25535654 | PMCID: PMC4308745
  • Pronk S, Lindahl E, Kasson P. Dynamic heterogeneity controls diffusion and viscosity near biological interfaces. Nature communications. 2014;5 3034. PMID: 24398864 | PMCID: PMC3971065
  • Purdy M, Bennett B, McIntire W, Khan A, Kasson P, Yeager M. Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. Current opinion in structural biology. 2014;27 138-148. PMID: 25238653
  • Russell C, Kasson P, Donis R, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis C, Garten R, Gnanakaran S, Hay S, Herfst S, Lewis N, Lloyd-Smith J, Macken C, Maurer-Stroh S, Neuhaus E, Parrish C, Pepin K, Shepard S, Smith D, Suarez D, Trock S, Widdowson M, George D, Lipsitch M, Bloom J. Improving pandemic influenza risk assessment. eLife. 2014;3 e03883. PMID: 25321142 | PMCID: PMC4199076
  • Computational biology in the cloud: methods and new insights from computing at scale. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2013; 451-3. PMID: 23424149
  • Domanska M, Wrona D, Kasson P. Multiphasic effects of cholesterol on influenza fusion kinetics reflect multiple mechanistic roles. Biophysical journal. 2013;105(6): 1383-7. PMID: 24047989 | PMCID: PMC3785876
  • Kasson P, Hess B, Lindahl E. Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions. Chemistry and physics of lipids. 2013;169 106-12. PMID: 23318532 | PMCID: PMC3631454
  • Larsson P, Kasson P. Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models. PLoS computational biology. 2013;9(3): e1002950. PMID: 23505359 | PMCID: PMC3591293
  • Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts M, Smith J, Kasson P, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England). 2013;29(7): 845-54. PMID: 23407358 | PMCID: PMC3605599
  • Receptor binding by influenza virus: using computational techniques to extend structural data. Biochemistry. 2012;51(12): 2359-65. PMID: 22409249
  • Kasson P, Lindahl E, Pande V. Water ordering at membrane interfaces controls fusion dynamics. Journal of the American Chemical Society. 2011;133(11): 3812-5. PMID: 21351772
  • Kasson P, Pande V. A bundling of viral fusion mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(10): 3827-8. PMID: 21368165 | PMCID: PMC3053970
  • Kasson P, Lindahl E, Pande V. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS computational biology. 2010;6(6): e1000829. PMID: 20585620 | PMCID: PMC2891707
  • Kasson P, Ensign D, Pande V. Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin. Journal of the American Chemical Society. 2009;131(32): 11338-40. PMID: 19637916 | PMCID: PMC2737089
  • Kasson P, Pande V. "Cross-graining": efficient multi-scale simulation via markov state models. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2009; 260-8. PMID: 19908378
  • Kasson P, Pande V. Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2009; 492-503. PMID: 19209725 | PMCID: PMC2811693
  • Kasson P, Pande V. Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin. Biophysical journal. 2008;95(7): L48-50. PMID: 18641068 | PMCID: PMC2547437
  • Ensign D, Kasson P, Pande V. Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. Journal of molecular biology. 2007;374(3): 806-16. PMID: 17950314 | PMCID: NIHMS34314
  • Kasson P, Pande V. Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics. PLoS computational biology. 2007;3(11): e220. PMID: 18020701 | PMCID: PMC2077900
  • Kasson P, Pande V. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2007; 40-50. PMID: 17992744
  • Kasson P, Zomorodian A, Park S, Singhal N, Guibas L, Pande V. Persistent voids: a new structural metric for membrane fusion. Bioinformatics (Oxford, England). 2007;23(14): 1753-9. PMID: 17488753
  • Kasson P, Kelley N, Singhal N, Vrljic M, Brunger A, Pande V. Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proceedings of the National Academy of Sciences of the United States of America. 2006;103(32): 11916-21. PMID: 16880392 | PMCID: PMC1567673
  • Kasson P, Huppa J, Davis M, Brunger A. A hybrid machine-learning approach for segmentation of protein localization data. Bioinformatics (Oxford, England). 2005;21(19): 3778-86. PMID: 16091410
  • Kasson P, Huppa J, Krogsgaard M, Davis M, Brunger A. Quantitative imaging of lymphocyte membrane protein reorganization and signaling. Biophysical journal. 2004;88(1): 579-89. PMID: 15501943 | PMCID: PMC1305035
  • Kasson P, Pande V. Molecular dynamics simulation of lipid reorientation at bilayer edges. Biophysical journal. 2004;86(6): 3744-9. PMID: 15189870 | PMCID: PMC1304275
  • Kasson P, Rabinowitz J, Schmitt L, Davis M, McConnell H. Kinetics of peptide binding to the class II MHC protein I-Ek. Biochemistry. 2000;39(5): 1048-58. PMID: 10653650
  • Rabinowitz J, Vrljic M, Kasson P, Liang M, Busch R, Boniface J, Davis M, McConnell H. Formation of a highly peptide-receptive state of class II MHC. Immunity. 1998;9(5): 699-709. PMID: 9846491