JUMNA (junction minimisation of nucleic acids)
作者： R. Lavery , K. Zakrzewska , H. Sklenar
DOI: 10.1016/0010-4655(95)00046-I
关键词: Nucleic acid 、 Force field (chemistry) 、 Computer science 、 Combinatorial search 、 Biological system
摘要: The latest version of JUMNA program for the energy optimisation nucleic acids and acid-ligand complexes is described. force field used, input output data, various options symmetry, conformational constraints mapping are discussed as well recent combinatorial search techniques.
harvard.edu
archives-ouvertes.fr
elsevier.com
sci-hub.se 参考文章(44)
O. Mauffret, B. Hartmann, O. Convert, R. Lavery, S. Fermandjian, The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse: Nuclear magnetic resonance and molecular simulation studies Journal of Molecular Biology. ,vol. 227, pp. 852- 875 ,(1992) , 10.1016/0022-2836(92)90227-B
Nobuhiro Gō, Harold A. Scheraga, Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules The Journal of Chemical Physics. ,vol. 51, pp. 4751- 4767 ,(1969) , 10.1063/1.1671863
R D Wells, Unusual DNA Structures ,(2011)
Richard Lavery, Krystyna Zakrzewska, Alberte Pullman, Optimized monopole expansions for the representation of the electrostatic properties of the nucleic acids Journal of Computational Chemistry. ,vol. 5, pp. 363- 373 ,(1984) , 10.1002/JCC.540050414
Nathalie Boutonnet, Xiaowen Hui, Krystyna Zakrzewska, Looking into the grooves of DNA. Biopolymers. ,vol. 33, pp. 479- 490 ,(1993) , 10.1002/BIP.360330314
E. Stofer, R. Lavery, Measuring the geometry of DNA grooves Biopolymers. ,vol. 34, pp. 337- 346 ,(1994) , 10.1002/BIP.360340305
Struther Arnott, D.W.L. Hukins, Optimised parameters for A-DNA and B-DNA Biochemical and Biophysical Research Communications. ,vol. 47, pp. 1504- 1509 ,(1972) , 10.1016/0006-291X(72)90243-4
Struther Arnott, D.W.L. Hukins, Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymers Journal of Molecular Biology. ,vol. 81, pp. 93- 105 ,(1973) , 10.1016/0022-2836(73)90182-4
Scott J. Weiner, Peter A. Kollman, David A. Case, U. Chandra Singh, Caterina Ghio, Guliano Alagona, Salvatore Profeta, Paul Weiner, A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS Journal of the American Chemical Society. ,vol. 106, pp. 765- 784 ,(1984) , 10.1021/JA00315A051
Stephan Diekmann, Definitions and nomenclature of nucleic acid structure parameters. Journal of Molecular Biology. ,vol. 205, pp. 787- 791 ,(1989) , 10.1016/0022-2836(89)90324-0