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Molecular dynamics

A Didactic Model of Macromolecular Crowding Effects on Protein Folding

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

published 03 Aug 2010

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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

published 19 Jul 2010

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

Maria Cristina De Rosa, Bruno Giardina, Caterina Bianchi, Cristiana Carelli Alinovi, Davide Pirolli, Gianfranco Ferraccioli, Maria De Santis, Gabriele Di Sante, Francesco Ria

published 14 Jul 2010

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

Flavia Autore, Julien R. C. Bergeron, Michael H. Malim, Franca Fraternali, Hendrik Huthoff

published 12 Jul 2010

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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

published 20 May 2010

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

Stefan Bernhard, Frank Noé

published 13 May 2010

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

Aruna Rajan, Lydia Freddolino, Klaus Schulten

published 15 Apr 2010

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

Piotr Ruchala, Mohamad Navab, Chun-Ling Jung, Susan Hama-Levy, Ewa D. Micewicz, Hai Luong, Jonathan E. Reyles, Shantanu Sharma, Alan J. Waring, Alan M. Fogelman, Robert I. Lehrer

published 14 Apr 2010

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Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins

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

published 07 Apr 2010

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

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

published 18 Feb 2010

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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

published 18 Feb 2010

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

Hao Zhang, Peng Wang, Nikitas Papangelopoulos, Ying Xu, Alessandro Sette, Philip E. Bourne, Ole Lund, Julia Ponomarenko, Morten Nielsen, Bjoern Peters

published 17 Feb 2010

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Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs

Diane Latawiec, Fernando Herrera, Alpan Bek, Valeria Losasso, Michela Candotti, Federico Benetti, Elvio Carlino, Agata Kranjc, Marco Lazzarino, Stefano Gustincich, Paolo Carloni, Giuseppe Legname

published 16 Feb 2010

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