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Molecular dynamics

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, Peter L. 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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How Cholesterol Constrains Glycolipid Conformation for Optimal Recognition of Alzheimer's β Amyloid Peptide (Aβ_1-40)

Nouara Yahi, Anaïs Aulas, Jacques Fantini

published 05 Feb 2010

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

Frans J. Walther, Alan J. Waring, Jose M. Hernandez-Juviel, Larry M. Gordon, Zhengdong Wang, Chun-Ling Jung, Piotr Ruchala, Andrew P. Clark, Wesley M. Smith, Shantanu Sharma, Robert H. Notter

published 13 Jan 2010

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

Li-Jun Yang, Jun Zou, Huan-Zhang Xie, Lin-Li Li, Yu-Quan Wei, Sheng-Yong Yang

published 24 Dec 2009

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Electroporating Fields Target Oxidatively Damaged Areas in the Cell Membrane

P. Thomas Vernier, Zachary A. Levine, Yu-Hsuan Wu, Vanessa Joubert, Matthew J. Ziegler, Lluis M. Mir, D. Peter Tieleman

published 23 Nov 2009

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