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Biophysical simulations

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin

Systematic Validation of Protein Force Fields against Experimental Data

Kresten Lindorff-Larsen, Paul Maragakis, [ ... ], David E. Shaw

Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak

Bakhtier Vasiev, Ariel Balter, [ ... ], Cornelis J. Weijer

Topological Data Analysis of Biological Aggregation Models

Chad M. Topaz, Lori Ziegelmeier, Tom Halverson

Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1

Min-Sun Park

Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements

Daniel Klose, Johann P. Klare, [ ... ], Heinz-Jürgen Steinhoff

Understanding Lignin-Degrading Reactions of Ligninolytic Enzymes: Binding Affinity and Interactional Profile

Ming Chen, Guangming Zeng, [ ... ], Gengxin Xie

Bare Bones Pattern Formation: A Core Regulatory Network in Varying Geometries Reproduces Major Features of Vertebrate Limb Development and Evolution

Jianfeng Zhu, Yong-Tao Zhang, Mark S. Alber, Stuart A. Newman

BioNet: A Python interface to NEURON for modeling large-scale networks

Sergey L. Gratiy, Yazan N. Billeh, [ ... ], Anton Arkhipov

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

Johannes Schöneberg, Frank Noé

Discovering Conformational Sub-States Relevant to Protein Function

Arvind Ramanathan, Andrej J. Savol, [ ... ], Chakra S. Chennubhotla

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc

Julien Michel, Rémi Cuchillo

Comparing Molecular Dynamics Force Fields in the Essential Subspace

Fernando Martín-García, Elena Papaleo, [ ... ], Kresten Lindorff-Larsen

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