FADRNÁ, Eva, Klára HLADEČKOVÁ a Jaroslav KOČA. Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2005, roč. 23, č. 2, s. 151-162. ISSN 0739-1102. |
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@article{588684, author = {Fadrná, Eva and Hladečková, Klára and Koča, Jaroslav}, article_location = {USA}, article_number = {2}, keywords = {Molecular dynamics; electrostatic interactions; endothelin-1}, language = {eng}, issn = {0739-1102}, journal = {Journal of Biomolecular Structure and Dynamics}, title = {Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study}, url = {http://www.jbsdonline.com/index.cfm?d=3021&c=4185&p=13084&do=detail}, volume = {23}, year = {2005} }
TY - JOUR ID - 588684 AU - Fadrná, Eva - Hladečková, Klára - Koča, Jaroslav PY - 2005 TI - Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study JF - Journal of Biomolecular Structure and Dynamics VL - 23 IS - 2 SP - 151-162 EP - 151-162 PB - Adenine Press SN - 07391102 KW - Molecular dynamics KW - electrostatic interactions KW - endothelin-1 UR - http://www.jbsdonline.com/index.cfm?d=3021&c=4185&p=13084&do=detail N2 - An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods -- residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used. ER -
FADRNÁ, Eva, Klára HLADEČKOVÁ a Jaroslav KOČA. Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. \textit{Journal of Biomolecular Structure and Dynamics}. USA: Adenine Press, 2005, roč.~23, č.~2, s.~151-162. ISSN~0739-1102.
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