Current Problems in Computer Simulation of Variability of Three-Dimensional Structure of DNA

[1]  Yan Zhao,et al.  Density Functionals for Noncovalent Interaction Energies of Biological Importance. , 2007, Journal of chemical theory and computation.

[2]  Daniel Svozil,et al.  DNA conformations and their sequence preferences , 2008, Nucleic acids research.

[3]  Alexander D. MacKerell,et al.  CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. , 2015, Biochimica et biophysica acta.

[4]  Jackson,et al.  Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. , 1992, Physical review. B, Condensed matter.

[5]  J. Šponer,et al.  Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. , 2015, Journal of chemical theory and computation.

[6]  Victor M. Anisimov,et al.  DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates , 2010 .

[7]  Bohdan Schneider,et al.  Automatic workflow for the classification of local DNA conformations , 2013, BMC Bioinformatics.

[8]  V. I. Poltev,et al.  DFT study of DNA sequence dependence at the level of dinucleoside monophosphates , 2011 .

[9]  D. Case,et al.  PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS , 2015, Nature Methods.

[10]  F. Matthias Bickelhaupt,et al.  Chemistry with ADF , 2001, J. Comput. Chem..

[11]  Victor M. Anisimov,et al.  DFT study of minimal fragments of nucleic acid single chain for explication of sequence dependence of DNA duplex conformation , 2009 .

[12]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[13]  A. Deriabina,et al.  Computational study of the molecular mechanisms of caffeine action: Caffeine complexes with adenosine receptors , 2010 .

[14]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[15]  Xiang-Jun Lu,et al.  Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures , 2009, Nucleic Acids Res..

[16]  William A Goddard,et al.  Universal Correction of Density Functional Theory to Include London Dispersion (up to Lr, Element 103). , 2012, The journal of physical chemistry letters.

[17]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[18]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[19]  V. Anisimov,et al.  Analysis of the conformational features of Watson–Crick duplex fragments by molecular mechanics and quantum mechanics methods , 2016, Biofizika.

[20]  V. Anisimov,et al.  Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments , 2018, Journal of Molecular Modeling.

[21]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[22]  Ranbir Singh,et al.  J. Mol. Struct. (Theochem) , 1996 .

[23]  N. Polteva,et al.  Some Problems of Computer Simulation of Non-Bonded Interactions in DNA , 2019, Biophysics.

[24]  D. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .

[25]  Victor M Anisimov,et al.  The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures. , 2014, Biopolymers.

[26]  John D. Westbrook,et al.  The Nucleic Acid Database: new features and capabilities , 2013, Nucleic Acids Res..

[27]  Andrzej Leś,et al.  DFT Study of B-like Conformations of Deoxydinucleoside Monophosphates Containing Gua and/or Cyt and their Complexes with Na+ Cation , 2008, Journal of Biomolecular Structure and Dynamics.

[28]  Stefan Grimme,et al.  Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..

[29]  Stefan Grimme,et al.  Effect of the damping function in dispersion corrected density functional theory , 2011, J. Comput. Chem..

[30]  S. F. Boys,et al.  The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .