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Biochemical simulations

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Estimating Absolute Configurational Entropies of Macromolecules: The Minimally Coupled Subspace Approach

Ulf Hensen, Oliver F. Lange, Helmut Grubmüller

Roles of Electrostatics and Conformation in Protein-Crystal Interactions

Paul V. Azzopardi, Jason O'Young, [ ... ], Graeme K. Hunter

Conformational Dynamics and Ligand Binding in the Multi-Domain Protein PDC109

Hyun Jin Kim, Moo Young Choi, Hyung J. Kim, Miguel Llinás

A Computational Study of a Recreated G Protein-GEF Reaction Intermediate Competent for Nucleotide Exchange: Fate of the Mg Ion

Mériam Ben Hamida-Rebaï, Charles H. Robert

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

Hao Zhang, Peng Wang, [ ... ], Bjoern Peters

Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs

Diane Latawiec, Fernando Herrera, [ ... ], Giuseppe Legname

Critical Structural and Functional Roles for the N-Terminal Insertion Sequence in Surfactant Protein B Analogs

Frans J. Walther, Alan J. Waring, [ ... ], Robert H. Notter

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

Sagar Indurkhya, Jacob Beal

A Conceptual Mathematical Model of the Dynamic Self-Organisation of Distinct Cellular Organelles

Bernd Binder, Andrean Goede, Nikolaus Berndt, Hermann-Georg Holzhütter

Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl

Li-Jun Yang, Jun Zou, [ ... ], Sheng-Yong Yang

Striated Muscle Regulation of Isometric Tension by Multiple Equilibria

Henry G. Zot, Javier E. Hasbun, Nguyen Van Minh

Electroporating Fields Target Oxidatively Damaged Areas in the Cell Membrane

P. Thomas Vernier, Zachary A. Levine, [ ... ], D. Peter Tieleman

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