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Coarse Grain

A coarsed grained protein-lipid model with application to high-density lipoprotein particles
Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, Klaus Schulten
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Aquaporin

Molecular basis of gating in aquaporin water channels
Yi Wang, Emad Tajkhorshid
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Sec Y

Dynamics of the Translocon SecY Investigated Through MD
James Gumbart, Klaus Schulten
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Gas Transport

Channel Mediated Gas Transport Across Lipid Membranes
Yi Wang, Klaus Schulten, Emad Tajkhorshid
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Ankyrin

Tertiary and Secondary Structure Elasticity of Ankyrin Repeats
Marcos Sotomayor, Klaus Schulten
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Titin Z1Z2-Telethonin

The Mechanical Stability of the Titin Z1Z2-Telethonin Complex as Revealed by Steered Molecular Dynamics
Eric H. Lee, Mu Gao, Matthias Wilmanns, Klaus Schulten
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ATP hydrolysis

A Computational Study of ATP Hydrolysis and Force Generation in PcrA Helicase
Markus Dittrich, Klaus Schulten
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F1

Simulated forced closure of an F1-ATPase subunit leads to rotation of the central stalk
Barry Isralewitz, Klaus Schulten
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Helicase

Structure-Based Model of a Stepping Motor on ssDNA: PcrA Helicase
Jin Yu, Taekjip Ha, Klaus Schulten
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Hydrogenase

Gas Migration Pathways Inside Proteins: Application to CpI hydrogenase
Jordi Cohen, Kwiseon Kim, Paul King, Michael Seibert, Klaus Schulten
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K Channel

Molecular Dynamics Simulation of a Voltage-Gated K+ Channel
Fatemeh Khalili-Araghi, Emad Tajkhorshid, Klaus Schulten
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Silica

Silica parametrization based on structural surface properties and wetting behavior for silica nanopore simulation
Eduardo Cruz-Chu, Aleksij Aksimentiev, Klaus Schulten
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Lactose Permease H+

Coupling of proton translocation and protein conformational change in E. coli lactose permease
Ying Yin, Morten Jensen, Emad Tajkhorshid, Klaus Schulten
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Myoglobin

Oxygen pathways in myoglobin
Anton Arkhipov, Jordi Cohen, Rosemary Braun, Klaus Schulten
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Lactose Permease Transport

The mechanism of sugar transport across E. coli lactose permease
Morten Jensen, Ying Yin, Emad Tajkhorshid, Klaus Shulten
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Virus

Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
Peter L. Freddolino, Anton S. Arkhipov, Klaus Schulten

Synthetic Nanopore

Exploring the Electro-Mechanical Properties of Single DNA Molecules with a Synthetic Nanopore
Jiunn B. Heng, Aleksei Aksimentiev, Elena Dimauro, Val Dimitrov, Qian Zhao, Chuen Ho, Patrick Marks, Yelena V. Grinkova, Steve Sligar, Klaus Schulten,
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Holliday Junction

Conformational Geometries of Holliday Junction in Conformer Transition
Jin Yu, Taekjip Ha, Klaus Schulten

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