"Jure\u010Dka, Petr" . "Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters" . "Otyepka, Michal" . "9" . "Cheatham, Thomas E III" . . . . . . . "Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters"@en . . . . "Luque, Javier F." . . . "RIV/00216224:14740/13:00069532!RIV14-MSM-14740___" . "14740" . . . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "10.1021/ct400154j" . "1"^^ . "MOLECULAR-DYNAMICS SIMULATIONS; PHOSPHORUS CHEMICAL-SHIFTS; SUGAR-PHOSPHATE BACKBONE; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; B-II TRANSITIONS; CRYSTAL-STRUCTURES; A-TRACT; CONFORMATIONAL PROPERTIES; RELATIVE FLEXIBILITY"@en . "1549-9618" . "Journal of Chemical Theory and Computation" . "Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters" . "http://pubs.acs.org/doi/abs/10.1021/ct400154j" . . . . . "6"^^ . "16"^^ . "Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters"@en . "[04B1EB1161A0]" . . . "We present a refinement of the backbone torsion parameters epsilon and zeta of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as epsilon zeta(OL1), were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7 (9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the epsilon zeta(OL1) refinement improves the backbone description of B-DNA double helices and the G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data." . . . "RIV/00216224:14740/13:00069532" . . "I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GAP208/10/1742)" . . . "\u0160poner, Ji\u0159\u00ED" . "111329" . "000319184800020" . "We present a refinement of the backbone torsion parameters epsilon and zeta of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as epsilon zeta(OL1), were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7 (9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the epsilon zeta(OL1) refinement improves the backbone description of B-DNA double helices and the G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data."@en . "5" . . "Zgarbova, Marie" . . .