http://www.cnr.it/ontology/cnr/individuo/prodotto/ID3368
Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case (Articolo in rivista)
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- Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case (Articolo in rivista) (literal)
- Anno
- 2008-01-01T00:00:00+01:00 (literal)
- Alternative label
Piccinini, E; Ceccarelli, M; Affinito, F; Brunetti, R; Jacoboni, C (2008)
Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case
in Journal of chemical theory and computation
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- Piccinini, E; Ceccarelli, M; Affinito, F; Brunetti, R; Jacoboni, C (literal)
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- \"[Piccinini, Enrico; Affinito, Fabio; Brunetti, Rossella; Jacoboni, Carlo] CNR, INFM, Natl Res Ctr Nanostructures & Biosyst Surfaces, I-41100 Modena, Italy; [Piccinini, Enrico] Univ Bologna, DEIS, Alma Mater Studiorum, I-40136 Bologna, Italy; [Ceccarelli, Matteo] Univ Cagliari, Dipartimento Fis, I-09042 Monserrato, Italy; [Ceccarelli, Matteo] Univ Cagliari, Sardinian Lab Computat Mat Sci SLACS, I-09042 Monserrato, Italy; [Affinito, Fabio; Brunetti, Rossella; Jacoboni, Carlo] Univ Modena, Dipartimento Fis, I-41100 Modena, Italy (literal)
- Titolo
- Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case (literal)
- Abstract
- The calculation of free-energy landscapes in proteins is a challenge for modern numerical simulations. As to the case of potassium ion channels is concerned, it is particularly interesting because of the nanometric dimensions of the selectivity filter, where the complex electrostatics is highly relevant. The present study aims at comparing three different techniques used to bias molecular dynamics simulations, namely Umbrella Sampling, Steered Molecular Dynamics, and Metadynamics, never applied all together in the past to the same channel protein. Our test case is represented by potassium ions permeating the selectivity filter of the KcsA channel. (literal)
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