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Biophysical simulations

The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics

Shivani Yaduvanshi, Rya Ero, Veerendra Kumar

published 05 Oct 2021

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Stochastic simulation algorithms for Interacting Particle Systems

Timothy C. Stutz, Alfonso Landeros, Jason Xu, Janet S. Sinsheimer, Mary Sehl, Kenneth Lange

published 02 Mar 2021

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Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis

Gabriel Rodrigues Coutinho Pereira, Bárbara de Azevedo Abrahim Vieira, Joelma Freire De Mesquita

published 25 Feb 2021

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Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades

Michael A. Rowland, Kevin R. Pilkiewicz, Michael L. Mayo

published 13 Jan 2021

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Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations

Arthur Voronin, Marie Weiel, Alexander Schug

published 16 Nov 2020

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BD5: An open HDF5-based data format to represent quantitative biological dynamics data

Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami

published 12 Aug 2020

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Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics

Philip Horx, Armin Geyer

published 13 Apr 2020

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Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach

Nematollah Gheibi, Mohamad Ghorbani, Hanifeh Shariatifar, Alireza Farasat

published 26 Mar 2020

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Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics

Gennady Gorin, Mengyu Wang, Ido Golding, Heng Xu

published 26 Mar 2020

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Using experimental gaming simulations to elicit risk mitigation behavioral strategies for agricultural disease management

Eric M. Clark, Scott C. Merrill, Luke Trinity, Gabriela Bucini, Nicholas Cheney, Ollin Langle-Chimal, Trisha Shrum, Christopher Koliba, Asim Zia, Julia M. Smith

published 17 Mar 2020

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Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6

Andrea E. Rawlings, Panah Liravi, Sybilla Corbett, Alex S. Holehouse, Sarah S. Staniland

published 25 Feb 2020

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Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods

Melissa S. Gildenberg, M. Todd Washington

published 18 Oct 2019

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Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation

Mahlet Z. Tamirat, Marika Koivu, Klaus Elenius, Mark S. Johnson

published 19 Sep 2019

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