P. Kasson

Shina Caroline Lynn Kamerlin, Peter M Kasson, P. Kasson, 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Ebolavirus Entry Requires a Compact Hydrophobic Fist at the Tip of the Fusion Loop

Per Larsson, P. Kasson, E. Nelson, 2014, Journal of Virology.

Formation of a highly peptide-receptive state of class II MHC.

M. Vrljic, M. Davis, P. Kasson, 1998, Immunity.

SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease

O. Troyanskaya, V. Nair, J. Hodgin, 2020 .

Development of COVID-19 vaccine using a dual Toll-like receptor ligand liposome adjuvant

W. Petri, P. Kasson, A. Pomés, 2021, NPJ vaccines.

SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease

Chandra L. Theesfeld, Rachel S. G. Sealfon, O. Troyanskaya, 2020, Kidney International.

SARS-CoV-2 receptor networks in diabetic kidney disease, BK-Virus nephropathy and COVID-19 associated acute kidney injury

Chandra L. Theesfeld, Rachel S. G. Sealfon, O. Troyanskaya, 2020, medRxiv.

Improving pandemic influenza risk assessment

James O Lloyd-Smith, Sebastian Maurer-Stroh, Samuel S. Shepard, 2014, eLife.

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

Y. Liu, E. Egelman, P. Kasson, 2018, Nature Communications.

Model for a novel membrane envelope in a filamentous hyperthermophilic virus

E. Egelman, Xiong Yu, P. Kasson, 2017, eLife.

Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide

Peter M. Kasson, Vijay S. Pande, V. Pande, 2006, Pacific Symposium on Biocomputing.

Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion.

Kenta Okamoto, P. Kasson, K. Zawada, 2018, Journal of molecular biology.

Quantitative imaging of lymphocyte membrane protein reorganization and signaling.

Mark M Davis, Axel T Brunger, Peter M Kasson, 2005, Biophysical journal.

Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics.

Ricardo J. Ferreira, P. Kasson, 2019, ACS infectious diseases.

pH Dependence of Zika Membrane Fusion Kinetics Reveals an Off-Pathway State

S. Boxer, P. Kasson, Elizabeth R. Webster, 2018, ACS central science.

Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy

Peter M. Kasson, Mark M. Davis, Mark M. Davis, 2004, 2004 International Conference on Image Processing, 2004. ICIP '04..

Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance

Peter M. Kasson, George A. Cortina, G. A. Cortina, 2016, Bioinform..

dataset to accompany Managing COVID-19 spread with voluntary public-health measures: Sweden as a case study for pandemic control

Shina Caroline Lynn Kamerlin, P. Kasson, Peter Kasson, 2020 .

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

Peter M. Kasson, Per Larsson, Per Larsson, 2013, PLoS Comput. Biol..

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails

Peter M. Kasson, Vijay S. Pande, Erik Lindahl, 2010, PLoS Comput. Biol..

Intervention strategies against COVID-19 and their estimated impact on Swedish healthcare capacity

Lander Willem, P. Kasson, Jasmine M Gardner, 2020, medRxiv.

Simulation-guided engineering of antibiotics for improved bacterial uptake

Ricardo J. Ferreira, P. Kasson, 2020 .

Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models

Peter M. Kasson, Vijay S. Pande, V. Pande, 2010, Pacific Symposium on Biocomputing.

Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics

Peter M. Kasson, Vijay S. Pande, V. Pande, 2007, PLoS Comput. Biol..

Gromacs User Manual Version 4.6

Peter M. Kasson, D. van der Spoel, Gerrit Groenhof, 2013 .

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin

Peter M. Kasson, Vijay S. Pande, V. Pande, 2008, Pacific Symposium on Biocomputing.

Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry

P. Kasson, Sai T. Bondalapati, Anjali Sengar, 2023, bioRxiv.

Single-virus fusion measurements yield an opportunistic model for SARS-CoV-2 fusion

P. Kasson, Sai T. Bondalapati, Anjali Sengar, 2021 .

A hybrid machine-learning approach for segmentation of protein localization data

Peter M. Kasson, Mark M. Davis, Mark M. Davis, 2005, Bioinform..

Adaptive Ensemble Biomolecular Applications at Scale

Shantenu Jha, Peter M. Kasson, Matteo Turilli, 2018, SN Computer Science.

Computational Biology in the Cloud: Methods and New Insights from Computing at Scale

Peter M. Kasson, P. Kasson, 2012, Pacific Symposium on Biocomputing.

Modeling biomolecular kinetics with large-scale simulation.

P. Kasson, 2021, Current opinion in structural biology.

Implementing Adaptive Ensemble Biomolecular Applications at Scale pdf

Shantenu Jha, Peter M. Kasson, Matteo Turilli, 2018, ArXiv.

Adaptive ensemble simulations of biomolecules.

Shantenu Jha, Peter M Kasson, S. Jha, 2018, Current opinion in structural biology.

Refinement of highly flexible protein structures using simulation-guided spectroscopy

Jennifer M. Hays, Marissa Kieber, Jason Z. Li, 2018, bioRxiv.

Computational methods to study enveloped viral entry.

P. Kasson, Alzbeta Tuerkova, 2021, Biochemical Society transactions.

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions.

E. Lindahl, B. Hess, P. Kasson, 2013, Chemistry and physics of lipids.

Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering

S. Boxer, P. Kasson, I. Goronzy, 2018, Chemical science.

Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.

Vijay S Pande, Peter M Kasson, Daniel L Ensign, 2009, Journal of the American Chemical Society.

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

Grant M. Rotskoff, Erik Lindahl, Magnus Lundborg, 2015, Journal of chemical theory and computation.

gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

Jennifer M. Hays, Peter M. Kasson, M. Eric Irrgang, 2018, bioRxiv.

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm250 Structural bioinformatics Persistent voids: a new structural metric for membrane fusion

Leonidas J. Guibas, Afra Zomorodian, Peter M. Kasson, 2022 .

Molecular dynamics simulation of lipid reorientation at bilayer edges.

V. Pande, P. Kasson, 2004, Biophysical journal.

Deformable modeling for improved calculation of molecular velocities from single-particle tracking

Peter M. Kasson, Mark M. Davis, Mark M. Davis, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

High-level software frameworks to surmount the challenge of 100x scaling for biomolecular simulation science

Shantenu Jha, Peter M. Kasson, S. Jha, 2015 .

Computational simulation of lipid bilayer reorientation at gaps

Peter M. Kasson, Vijay S. Pande, V. Pande, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Precise Triggering and Chemical Control of Single-Virus Fusion within Endosomes

Kenta Okamoto, P. Kasson, S. Haldar, 2020, Journal of Virology.

A bundling of viral fusion mechanisms

V. Pande, P. Kasson, 2011, Proceedings of the National Academy of Sciences.

Adaptive Ensemble Biomolecular Applications at Scale

Shantenu Jha, Matteo Turilli, Vivek Balasubramanian, 2018, SN Computer Science.

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

M. E. Irrgang, P. Kasson, C. Davis, 2021, bioRxiv.

KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes.

P. Kasson, S. C. Kamerlin, Rory M. Crean, 2023, Journal of Chemical Physics.

Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.

V. Pande, D. Ensign, P. Kasson, 2009, Journal of the American Chemical Society.

Copernicus: A new paradigm for parallel adaptive molecular dynamics

Peter M. Kasson, Vijay S. Pande, Berk Hess, 2011, 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC).

Persistent voids: a new structural metric for membrane fusion

V. Pande, A. Zomorodian, Nina Singhal, 2007, Bioinform..

The ACE2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion

G. Morbioli, P. Kasson, Anjali Sengar, 2022, bioRxiv.

Influenza Virus Membrane Fusion Is Promoted by the Endosome-Resident Phospholipid Bis(monoacylglycero)phosphate

P. Kasson, A. V. Villamil Giraldo, Steinar Mannsverk, 2022, bioRxiv.