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Biochemical simulations

Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation

Stefan Bernhard, Frank Noé

A Two-Dimensional Simulation Model of the Bicoid Gradient in Drosophila

Jingyuan Deng, Wei Wang, Long Jason Lu, Jun Ma

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Jenna L. Morgan, Aaron E. Darling, Jonathan A. Eisen

Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding

Aruna Rajan, Peter L. Freddolino, Klaus Schulten

Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

Erik J. Thompson, Allison J. DePaul, Sarav S. Patel, Eric J. Sorin

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

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