| scholarly article | Q13442814 |
| P5530 | Altmetric DOI | 10.1038/NMETH.3658 |
| P6409 | CORE ID | 41828626 |
| P6179 | Dimensions Publication ID | 1050825171 |
| P356 | DOI | 10.1038/NMETH.3658 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1038/nmeth.3658 |
| P953 | full work available at URL | http://eprints.whiterose.ac.uk/100211/ |
| P932 | PMC publication ID | 4700514 |
| P698 | PubMed publication ID | 26569599 |
| P5875 | ResearchGate publication ID | 284022716 |
| P1154 | Scopus EID | 2-s2.0-84955684595 |
| P50 | author | Michele Vendruscolo | Q28322492 |
| Agnes Noy | Q54636105 | ||
| Pablo D. Dans | Q55457363 | ||
| Alexandra Balaceanu | Q56420375 | ||
| Federica Battistini | Q56420376 | ||
| Ignacio Faustino | Q56420377 | ||
| Sarah A Harris | Q56441425 | ||
| Modesto Orozco | Q63487839 | ||
| Alberto Perez | Q63852517 | ||
| Carlos González | Q40859618 | ||
| Guillem Portella | Q41047555 | ||
| Josep Lluís Gelpí | Q41728401 | ||
| David A. Case | Q42718941 | ||
| P2093 | author name string | David A Case | |
| Charles A Laughton | |||
| Ivan Ivani | |||
| Adam Hospital | |||
| Pau Andrio | |||
| Jürgen Walther | |||
| Ramon Goñi | |||
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| Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs | Q58445500 | ||
| Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), andab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock | Q58445837 | ||
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| Optimised parameters for A-DNA and B-DNA | Q70409700 | ||
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| Exploring the Essential Dynamics of B-DNA | Q86864345 | ||
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| A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. | Q33566434 | ||
| A measure of bending in nucleic acids structures applied to A-tract DNA. | Q33889278 | ||
| Dielectric response of triplex DNA in ionic solution from simulations | Q34047375 | ||
| Direct measurement of the dielectric polarization properties of DNA. | Q34144701 | ||
| Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps | Q34188047 | ||
| On the absence of intrahelical DNA dynamics on the μs to ms timescale | Q34433149 | ||
| NAFlex: a web server for the study of nucleic acid flexibility. | Q34728020 | ||
| Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions | Q34975596 | ||
| Theoretical methods for the simulation of nucleic acids. | Q35606425 | ||
| Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. | Q36422866 | ||
| Kinking the double helix by bending deformation | Q36509154 | ||
| Towards a molecular dynamics consensus view of B-DNA flexibility | Q36633176 | ||
| Torsional directed walks, entropic elasticity, and DNA twist stiffness | Q36818468 | ||
| Frontiers in molecular dynamics simulations of DNA. | Q37914843 | ||
| Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles | Q38389887 | ||
| DNA and its counterions: a molecular dynamics study | Q39946368 | ||
| Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields | Q39949431 | ||
| Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the "Gold Standard," CCSD(T) at the Complete Basis Set Limit? | Q40303956 | ||
| Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. | Q41476736 | ||
| All-atom crystal simulations of DNA and RNA duplexes | Q41962161 | ||
| On the use of orientational restraints and symmetry corrections in alchemical free energy calculations | Q42106721 | ||
| Exploring polymorphisms in B-DNA helical conformations. | Q42370883 | ||
| Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters | Q42627952 | ||
| How stiff is DNA? | Q42709051 | ||
| Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies. | Q43827809 | ||
| Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study. | Q46565646 | ||
| Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. | Q46892685 | ||
| NMR: prediction of molecular alignment from structure using the PALES software. | Q48590571 | ||
| Dynamics of B-DNA on the microsecond time scale. | Q50141941 | ||
| Sequence-dependent elastic properties of DNA. | Q52077990 | ||
| MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. | Q53383167 | ||
| P433 | issue | 1 | |
| P921 | main subject | force field | Q1341441 |
| P304 | page(s) | 55-58 | |
| P577 | publication date | 2015-11-16 | |
| P1433 | published in | Nature Methods | Q680640 |
| P1476 | title | Parmbsc1: a refined force field for DNA simulations | |
| P478 | volume | 13 |
| Q48159973 | A DNA structural alphabet provides new insight into DNA flexibility |
| Q92761503 | A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level |
| Q92995703 | A trade-off for covalent and intercalation binding modes: a case study for Copper (II) ions and singly modified DNA nucleoside |
| Q50041152 | AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. |
| Q48043818 | Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA. |
| Q26738495 | Advances in the characterization of RNA-binding proteins |
| Q89113644 | Allosterism and signal transfer in DNA |
| Q27301352 | Assessing the Current State of Amber Force Field Modifications for DNA |
| Q64067249 | Automated cryo-EM structure refinement using correlation-driven molecular dynamics |
| Q27325057 | BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data |
| Q92963099 | Bending of DNA duplexes with mutation motifs |
| Q99345179 | Binding mode multiplicity and multiscale chirality in the supramolecular assembly of DNA and a π-conjugated polymer |
| Q48042182 | Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments |
| Q37618021 | Changing POU dimerization preferences converts Oct6 into a pluripotency inducer |
| Q96127688 | Colibactin DNA-damage signature indicates mutational impact in colorectal cancer |
| Q30853605 | Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. |
| Q90384557 | Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors |
| Q33580368 | Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates |
| Q40957394 | Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome |
| Q49981680 | Construction and Structure Studies of DNA-bipyridine Complexes as Versatile Scaffolds for Site-Specific Incorporation of Metal Ions into DNA. |
| Q39036608 | Contributions of Sequence to the Higher-Order Structures of DNA. |
| Q89870684 | Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution |
| Q99608462 | DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site |
| Q41216018 | DNA mutation motifs in the genes associated with inherited diseases. |
| Q55171599 | DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations. |
| Q92202991 | DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region |
| Q39144482 | DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. |
| Q38687819 | Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes. |
| Q58611534 | Detection and identification of genetic material via single-molecule conductance |
| Q92167434 | Divalent cations promote TALE DNA-binding specificity |
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| Q92891069 | Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts |
| Q59132487 | Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA |
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| Q55495686 | ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma. |
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| Q90019116 | Elucidating the influence of linker histone variants on chromatosome dynamics and energetics |
| Q58702043 | Engineering a responsive DNA triple helix into an octahedral DNA nanostructure for a reversible opening/closing switching mechanism: a computational and experimental integrated study |
| Q46912958 | Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding |
| Q90484475 | Exploring potentially alternative non-canonical DNA duplex structures through simulation |
| Q33912756 | Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. |
| Q42092575 | How accurate are accurate force-fields for B-DNA? |
| Q64986214 | How methyl-sugar interactions determine DNA structure and flexibility. |
| Q47143904 | How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. |
| Q41483588 | Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process. |
| Q92571037 | Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations |
| Q92156239 | In Silico and In Cell Analysis of Openable DNA Nanocages for miRNA Silencing |
| Q33701399 | Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. |
| Q47161639 | Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level |
| Q50324165 | Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA. |
| Q33557556 | Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics |
| Q60950340 | Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design |
| Q92932151 | Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes |
| Q41931128 | Long-timescale dynamics of the Drew-Dickerson dodecamer. |
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| Q33557641 | Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays |
| Q47998413 | Martini Coarse-Grained Force Field: Extension to RNA. |
| Q59807633 | Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics |
| Q64067802 | Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond |
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| Q47289880 | Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain suggest a role of the lever-arm mobility in transcriptional output. |
| Q47135560 | Molecular simulations of cellular processes. |
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| Q89575574 | Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding |
| Q48046200 | Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA. |
| Q58196257 | Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor |
| Q48041687 | Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics. |
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