Computational Simulation of Lipid Bilayer Reorientation at Gaps. - Peter M. Kasson; Vijay S. Pande (CSB, 2003)

Quantitative Analysis of Membrane Protein Localization and Signaling. - Peter M. Kasson; Johannes B. Huppa; Mark M. Davis; Axel T. Brünger (CSB, 2004)

Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy. - Peter M. Kasson; Johannes B. Huppa; Mark M. Davis; Axel T. Brünger (ICIP, 2004)

Deformable Modeling for Improved Calculation of Molecular Velocities from Single-Particle Tracking. - Peter M. Kasson; Mark M. Davis; Axel T. Brünger (CSB, 2005)

A hybrid machine-learning approach for segmentation of protein localization data. - Peter M. Kasson; Johannes B. Huppa; Mark M. Davis; Axel T. Brünger (Bioinform., 2005)

Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide. - Peter M. Kasson; Vijay S. Pande (Pacific Symposium on Biocomputing, 2007)

Persistent voids: a new structural metric for membrane fusion. - Peter M. Kasson; Afra Zomorodian; Sanghyun Park; Nina Singhal; Leonidas J. Guibas; Vijay S. Pande (Bioinform., 2007)

Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics. - Peter M. Kasson; Vijay S. Pande (PLoS Comput. Biol., 2007)

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. - Peter M. Kasson; Vijay S. Pande (Pacific Symposium on Biocomputing, 2009)

Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models. - Peter M. Kasson; Vijay S. Pande (Pacific Symposium on Biocomputing, 2010)

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. - Peter M. Kasson; Erik Lindahl; Vijay S. Pande (PLoS Comput. Biol., 2010)

Copernicus: a new paradigm for parallel adaptive molecular dynamics. - Sander Pronk; Per Larsson; Iman Pouya; Gregory R. Bowman; Imran S. Haque; Kyle Beauchamp; Berk Hess; Vijay S. Pande; Peter M. Kasson; Erik Lindahl (SC, 2011)

Computational Biology in the Cloud: Methods and New Insights from Computing at Scale. - Peter M. Kasson (Pacific Symposium on Biocomputing, 2013)

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. - Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R. Shirts; Jeremy C. Smith; Peter M. Kasson; David van der Spoel; Berk Hess; Erik Lindahl (Bioinform., 2013)

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models. - Per Larsson; Peter M. Kasson (PLoS Comput. Biol., 2013)

Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance. - George A. Cortina; Peter M. Kasson (Bioinform., 2016)

gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations. - M. Eric Irrgang; Jennifer M. Hays; Peter M. Kasson (Bioinform., 2018)

Implementing Adaptive Ensemble Biomolecular Applications at Scale. - Vivek Balasubramanian; Travis Jensen; Matteo Turilli; Peter M. Kasson; Michael R. Shirts; Shantenu Jha (CoRR, 2018)

Adaptive Ensemble Biomolecular Applications at Scale. - Vivek Balasubramanian; Travis Jensen; Matteo Turilli; Peter M. Kasson; Michael R. Shirts; Shantenu Jha (SN Comput. Sci., 2020)

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support. - M. Eric Irrgang; Caroline Davis; Peter M. Kasson (PLoS Comput. Biol., 2022)

Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses. - Jamel Simpson; Peter M. Kasson (PLoS Comput. Biol., 2025)