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Biophysical simulations

Dynamic Regulation of Phenylalanine Hydroxylase by Simulated Redox Manipulation

Julian E. Fuchs, Roland G. Huber, [ ... ], Klaus R. Liedl

Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes

Basak Isin, Guillermina Estiu, Olaf Wiest, Zoltán N. Oltvai

Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

Ivan Komarov, Roshan M. D'Souza

Mapping Paratope on Antithrombotic Antibody 6B4 to Epitope on Platelet Glycoprotein Ibalpha via Molecular Dynamic Simulations

Xiang Fang, Ying Fang, [ ... ], Jianhua Wu

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

Julien Michel, Rémi Cuchillo

Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics

Gennady M. Verkhivker

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

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

Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

Ivan Komarov, Roshan M. D’Souza, Jose-Juan Tapia

Investigation of the Acetylation Mechanism by GCN5 Histone Acetyltransferase

Junfeng Jiang, Junyan Lu, [ ... ], Cheng Luo

Stochastic Modeling for the Expression of a Gene Regulated by Competing Transcription Factors

Hsih-Te Yang, Minoru S. H. Ko

Systematic Validation of Protein Force Fields against Experimental Data

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

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

Jingwei Weng, Kangnian Fan, Wenning Wang

Combining Optimal Control Theory and Molecular Dynamics for Protein Folding

Yaman Arkun, Mert Gur

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