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Biophysical simulations

Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing

Michael T. Zimmermann, Raul Urrutia, [ ... ], Eric W. Klee

CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

Atefeh Kazeroonian, Fabian Fröhlich, [ ... ], Jan Hasenauer

AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics

Shray Vats, Raitis Bobrovs, Pär Söderhjelm, Soumendranath Bhakat

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

Stephen A. Wells, Marc W. van der Kamp, John D. McGeagh, Adrian J. Mulholland

Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations

Yan Wang, Myung Hee Kim, [ ... ], Nam-Joon Cho

cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems

Marco S. Nobile, Paolo Cazzaniga, [ ... ], Giancarlo Mauri

Structural Insights into RbmA, a Biofilm Scaffolding Protein of V. Cholerae

Manuel Maestre-Reyna, Wen-Jin Wu, Andrew H.-J. Wang

Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations

Hong Zhu, Shiyan Xiao, Haojun Liang

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

Andrew T. Fenley, Hari S. Muddana, Michael K. Gilson

Filamentous Biopolymers on Surfaces: Atomic Force Microscopy Images Compared with Brownian Dynamics Simulation of Filament Deposition

Norbert Mücke, Konstantin Klenin, [ ... ], Jörg Langowski

The Conformational Transition Pathways of ATP-Binding Cassette Transporter BtuCD Revealed by Targeted Molecular Dynamics Simulation

Jingwei Weng, Kangnian Fan, Wenning Wang

Spiral and Rotor Patterns Produced by Fairy Ring Fungi

Nathaniel Karst, David Dralle, Sally Thompson

Aggregation of Lipid-Anchored Full-Length H-Ras in Lipid Bilayers: Simulations with the MARTINI Force Field

Hualin Li, Alemayehu A. Gorfe

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