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Molecular dynamics

SH3 Domain-Peptide Binding Energy Calculations Based on Structural Ensemble and Multiple Peptide Templates

Seungpyo Hong, Taesu Chung, Dongsup Kim

Molecular Modeling Study for Interaction between Bacillus subtilis Obg and Nucleotides

Yuno Lee, Woo Young Bang, [ ... ], Keun Woo Lee

Insights in 17β-HSD1 Enzyme Kinetics and Ligand Binding by Dynamic Motion Investigation

Matthias Negri, Maurizio Recanatini, Rolf W. Hartmann

A Didactic Model of Macromolecular Crowding Effects on Protein Folding

Douglas Tsao, Allen P. Minton, Nikolay V. Dokholyan

A Comparative Approach Linking Molecular Dynamics of Altered Peptide Ligands and MHC with In Vivo Immune Responses

Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner, Michelle M. Epstein

Modeling the Ternary Complex TCR-Vβ/CollagenII(261–273)/HLA-DR4 Associated with Rheumatoid Arthritis

Maria Cristina De Rosa, Bruno Giardina, [ ... ], Francesco Ria

Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations

Flavia Autore, Julien R. C. Bergeron, [ ... ], Hendrik Huthoff

The Role of Phe82 and Phe351 in Auxin-Induced Substrate Perception by TIR1 Ubiquitin Ligase: A Novel Insight from Molecular Dynamics Simulations

Ge-Fei Hao, Guang-Fu Yang

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

Stefan Bernhard, Frank Noé

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

Aruna Rajan, Lydia Freddolino, Klaus Schulten

Oxpholipin 11D: An Anti-Inflammatory Peptide That Binds Cholesterol and Oxidized Phospholipids

Piotr Ruchala, Mohamad Navab, [ ... ], Robert I. Lehrer

Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

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

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

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

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