TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami
暂无分享,去创建一个
Lorenzo Rovigatti | Flavio Romano | Erik Poppleton | Antonio Suma | Cristian Micheletti | Petr Šulc | Michael Matthies | Jonathan P K Doye | Ard A Louis | J. Doye | C. Micheletti | A. Louis | M. Matthies | P. Šulc | F. Romano | A. Suma | L. Rovigatti | Erik Poppleton
[1] Hao Yan,et al. Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.
[2] Enzo Orlandini,et al. Knotting and Unknotting Dynamics of DNA Strands in Nanochannels , 2014 .
[3] Faisal A. Aldaye,et al. Assembling Materials with DNA as the Guide , 2008, Science.
[4] Hao Yan,et al. Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures , 2009, DNA.
[5] Sarah A. Harris,et al. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA , 2011, Nucleic acids research.
[6] F. Sciortino,et al. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars. , 2016, The Journal of chemical physics.
[7] Wah Chiu,et al. Structural diversity of supercoiled DNA , 2015, Nature Communications.
[8] J. Maddocks,et al. A Continuum Rod Model of Sequence-Dependent DNA Structure , 1996 .
[9] Alexey Savelyev,et al. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. , 2009, Biophysical journal.
[10] J. Maddocks,et al. Sequence-Dependent Persistence Lengths of DNA. , 2017, Journal of chemical theory and computation.
[11] F. B. Fuller. The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[12] Mark Bathe,et al. A primer to scaffolded DNA origami , 2011, Nature Methods.
[13] V. Zhurkin,et al. Modeling DNA deformations. , 2000, Current opinion in structural biology.
[14] Flavio Romano,et al. A nucleotide-level coarse-grained model of RNA. , 2014, The Journal of chemical physics.
[15] Giovanni Dietler,et al. Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases , 2011, Proceedings of the National Academy of Sciences.
[16] Julien Dorier,et al. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes , 2013, Nucleic acids research.
[17] David L. Beveridge,et al. Molecular dynamics studies of DNA , 1994 .
[18] Davide Marenduzzo,et al. DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting , 2009, Proceedings of the National Academy of Sciences.
[19] Flavio Romano,et al. Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model. , 2017, ACS nano.
[20] Jejoong Yoo,et al. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation , 2016, Nucleic acids research.
[21] R L Jernigan,et al. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. , 1993, Journal of molecular biology.
[22] N R Cozzarelli,et al. Probability of DNA knotting and the effective diameter of the DNA double helix. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[23] D. Schwartz,et al. A coarse grain model for DNA. , 2007, The Journal of chemical physics.
[24] Adam H. Marblestone,et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno , 2009, Nucleic acids research.
[25] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[26] K Shishido,et al. The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant. , 1989, Nucleic acids research.
[27] Francis W. Starr,et al. Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments , 2016, Scientific Reports.
[28] Gregory A. Voth,et al. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.
[29] Tine Curk,et al. Coarse-grained simulation of DNA using LAMMPS , 2018, The European physical journal. E, Soft matter.
[30] Jejoong Yoo,et al. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations , 2013, Proceedings of the National Academy of Sciences.
[31] M. Bathe,et al. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures , 2011, Nucleic acids research.
[32] J. Doye,et al. Sequence-dependent thermodynamics of a coarse-grained DNA model. , 2012, The Journal of chemical physics.
[33] M. Wasielewski,et al. Conformationally Gated Charge Transfer in DNA Three-Way Junctions. , 2015, The journal of physical chemistry letters.
[34] Davide Marenduzzo,et al. Topological friction strongly affects viral DNA ejection , 2013, Proceedings of the National Academy of Sciences.
[35] Davide Marenduzzo,et al. Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness. , 2003, Journal of molecular biology.
[36] C. Micheletti,et al. Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking , 2018, bioRxiv.
[37] T. Schlick. Molecular modeling and simulation , 2002 .
[38] A. Stasiak,et al. Formation of knots in partially replicated DNA molecules. , 1999, Journal of molecular biology.
[39] Veikko Linko,et al. Automated design of DNA origami , 2016, Nature Biotechnology.
[40] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[41] K. Klenin,et al. Computation of writhe in modeling of supercoiled DNA. , 2000, Biopolymers.
[42] Wah Chiu,et al. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. , 2019, ACS nano.
[43] C. Micheletti,et al. Inferring the diameter of a biopolymer from its stretching response. , 2005, Biophysical journal.
[44] Giovanni Bussi,et al. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs , 2017, Nucleic acids research.
[45] Jonathan P. K. Doye,et al. Direct Simulation of the Self-Assembly of a Small DNA Origami. , 2016, ACS nano.
[46] J. Doye,et al. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. , 2010, The Journal of chemical physics.
[47] Richard A. Cunha,et al. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview , 2018, Chemical reviews.
[48] James H. White. Self-Linking and the Gauss Integral in Higher Dimensions , 1969 .
[49] Antonio Suma,et al. Pore translocation of knotted DNA rings , 2017, Proceedings of the National Academy of Sciences.
[50] Sergio Pantano,et al. A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. , 2010, Journal of chemical theory and computation.
[51] Baoquan Ding,et al. A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo , 2018, Nature Biotechnology.
[52] Tamar Schlick,et al. Molecular Modeling and Simulation: An Interdisciplinary Guide , 2010 .
[53] Huilin Li,et al. Diamond family of nanoparticle superlattices , 2016, Science.
[54] Modesto Orozco,et al. Multiscale simulation of DNA. , 2016, Current opinion in structural biology.
[55] Alexey Savelyev,et al. Recent successes in coarse‐grained modeling of DNA , 2013 .
[56] A. Stasiak,et al. DNA supercoiling and its role in DNA decatenation and unknotting , 2009, Nucleic acids research.
[57] C. Micheletti,et al. Knotting dynamics of DNA chains of different length confined in nanochannels , 2015, Journal of physics. Condensed matter : an Institute of Physics journal.
[58] Tim Liedl,et al. Force-Induced Unravelling of DNA Origami. , 2018, ACS nano.
[59] A. Louis,et al. Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation , 2016, Nucleic acids research.
[60] Ronald C. Read,et al. The knot book: An elementary introduction to the mathematical theory of knots , 1997, Complex..
[61] Fei Zhang,et al. DNA Origami: Scaffolds for Creating Higher Order Structures. , 2017, Chemical reviews.
[62] Erwin Frey,et al. Excluded volume effects on semiflexible ring polymers. , 2009, Nano letters.
[63] Antonio Suma,et al. Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity. , 2015, ACS macro letters.