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Biophysical simulations

Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium

L. Michel Espinoza-Fonseca, David D. Thomas

Understanding Lignin-Degrading Reactions of Ligninolytic Enzymes: Binding Affinity and Interactional Profile

Ming Chen, Guangming Zeng, [ ... ], Gengxin Xie

Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1

Debin Mao, Shouqin Lü, [ ... ], Mian Long

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

Dirk Matthes, Vytautas Gapsys, Venita Daebel, Bert L. de Groot

Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization

Honda Naoki, Shinichi Nakamuta, Kozo Kaibuchi, Shin Ishii

Discovering Conformational Sub-States Relevant to Protein Function

Arvind Ramanathan, Andrej J. Savol, [ ... ], Chakra S. Chennubhotla

Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations

Shouqin Lü, Yan Zhang, Mian Long

Characterization of Membrane Potential Dependency of Mitochondrial Ca²⁺ Uptake by an Improved Biophysical Model of Mitochondrial Ca²⁺ Uniporter

Ranjan K. Pradhan, Feng Qi, Daniel A. Beard, Ranjan K. Dash

Bare Bones Pattern Formation: A Core Regulatory Network in Varying Geometries Reproduces Major Features of Vertebrate Limb Development and Evolution

Jianfeng Zhu, Yong-Tao Zhang, Mark S. Alber, Stuart A. Newman

Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak

Bakhtier Vasiev, Ariel Balter, [ ... ], Cornelis J. Weijer

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

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

Li-Jun Yang, Jun Zou, [ ... ], Sheng-Yong Yang

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