Relevant bibliographies by topics / Bias Exchange Metadynamics

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  1. Journal articles
  2. Dissertations / Theses

Academic literature on the topic 'Bias Exchange Metadynamics'

Author: Grafiati
Published: 14 March 2023

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Journal articles on the topic "Bias Exchange Metadynamics"

1

Baftizadeh Baghal, Fahimeh, Xevi Biarnes, Fabio Pietrucci, Alessandro Laio, and Fabio Affinito. "Simulation of Amyloid Nucleation with Bias-Exchange Metadynamics." Biophysical Journal 102, no. 3 (January 2012): 242a. http://dx.doi.org/10.1016/j.bpj.2011.11.1336.

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2

Singh, Richa, Rohit Bansal, Anurag Singh Rathore, and Gaurav Goel. "Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics." Biophysical Journal 112, no. 8 (April 2017): 1571–85. http://dx.doi.org/10.1016/j.bpj.2017.03.015.

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3

Bulo, Rosa E., Hans Van Schoot, Daniel Rohr, and Carine Michel. "Bias-exchange metadynamics applied to the study of chemical reactivity." International Journal of Quantum Chemistry 110, no. 12 (March 10, 2010): 2299–307. http://dx.doi.org/10.1002/qua.22554.

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4

Baftizadeh, Fahimeh, Pilar Cossio, Fabio Pietrucci, and Alessandro Laio. "Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations." Current Physical Chemistry 2, no. 1 (January 1, 2012): 79–91. http://dx.doi.org/10.2174/1877946811202010079.

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5

Baftizadeh, Fahimeh, Pilar Cossio, Fabio Pietrucci, and Alessandro Laio. "Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations." Current Physical Chemistrye 2, no. 1 (January 1, 2012): 79–91. http://dx.doi.org/10.2174/1877947611202010079.

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6

Cao, Zanxia, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, and Yaoqi Zhou. "Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids." International Journal of Molecular Sciences 19, no. 3 (March 16, 2018): 885. http://dx.doi.org/10.3390/ijms19030885.

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7

Todorova, Nevena, Fabrizio Marinelli, Stefano Piana, and Irene Yarovsky. "Exploring the Folding Free Energy Landscape of Insulin Using Bias Exchange Metadynamics." Journal of Physical Chemistry B 113, no. 11 (March 19, 2009): 3556–64. http://dx.doi.org/10.1021/jp809776v.

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8

Furini, Simone, Paolo Barbini, and Carmen Domene. "Conduction and Selectivity in Na+ Channels Analyzed by Bias-Exchange Metadynamics Simulations." Biophysical Journal 108, no. 2 (January 2015): 490a. http://dx.doi.org/10.1016/j.bpj.2014.11.2682.

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9

Mehrabian, Hadi, and Bernhardt L. Trout. "In Silico Engineering of Hydrate Anti-agglomerant Molecules Using Bias-Exchange Metadynamics Simulations." Journal of Physical Chemistry C 124, no. 35 (August 5, 2020): 18983–92. http://dx.doi.org/10.1021/acs.jpcc.0c03251.

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10

Ansari, Samiul M., Andrea Coletta, Katrine Kirkeby Skeby, Jesper Sørensen, Birgit Schiøtt, and David S. Palmer. "Allosteric-Activation Mechanism of Bovine Chymosin Revealed by Bias-Exchange Metadynamics and Molecular Dynamics Simulations." Journal of Physical Chemistry B 120, no. 40 (September 29, 2016): 10453–62. http://dx.doi.org/10.1021/acs.jpcb.6b07491.

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Dissertations / Theses on the topic "Bias Exchange Metadynamics"

1

Bisha, Ina. "Atomistic Study of Structural and Functional Properties of Membrane Proteins." Doctoral thesis, SISSA, 2014. http://hdl.handle.net/20.500.11767/3893.

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Abstract:
Living cells exploit membrane proteins to carry out crucial functions like transport of nutrients, signal transduction, energy conversion, etc. Recently, the remarkable and continuous improvement of computational algorithms and power allowed simulating and investigating relevant aspects of the mechanisms of this important class of proteins. In this thesis we focused on the study of two membrane proteins: a transporter and an ion channel. Firstly, we investigated the bacterial homologue of Sodium Galactose Transporter (SGLT), which plays an important role in the accumulation of sugars (i.e. glucose or galactose) inside cells, assuring a correct intestinal absorption and renal re-absorption. Using enhanced sampling techniques, we focused in understanding selected aspects of its transport mechanism. First, we identified a stable Na+ ion binding site, which was not solved crystallographically. Second, based on the results of the first study, we investigated the mechanism of the binding/release of both ligands to/from the protein in the inward-facing conformation and their interplay during this process. Finally, we also worked on another membrane protein: the Cyclic Nucleotide-Gated (CNG) channel. Using a chimera, the NaK2CNG mimic, we investigated the structural basis of the linkage among gating and permeation and of the voltage dependence shown by this channel. Large-scale molecular dynamics (MD) simulations, together with electrophysiology and X-ray crystallography, have been used to study the permeation mechanism of this mimic as a model system of CNG in presence of different alkalications.
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