| review article | Q7318358 |
| scholarly article | Q13442814 |
| P356 | DOI | 10.1002/0471142700.NC0710S56 |
| P698 | PubMed publication ID | 25606980 |
| P50 | author | Thomas E. Cheatham, III | Q62676269 |
| P2093 | author name string | Christina Bergonzo | |
| Rodrigo Galindo-Murillo | |||
| P2860 | cites work | Molecular dynamics simulations of sarcin-ricin rRNA motif. | Q25255860 |
| High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations | Q27014673 | ||
| Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure | Q27681249 | ||
| Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers | Q29615408 | ||
| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 | ||
| Exploring protein native states and large-scale conformational changes with a modified generalized born model | Q29617088 | ||
| Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations | Q30544923 | ||
| Validation of the 53A6 GROMOS force field | Q30986204 | ||
| Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis | Q30990709 | ||
| PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | Q31026348 | ||
| Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids | Q33344193 | ||
| Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results | Q33537644 | ||
| A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. | Q33566434 | ||
| A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation | Q33907726 | ||
| Development and current status of the CHARMM force field for nucleic acids. | Q34106357 | ||
| Toward a consensus view of duplex RNA flexibility | Q34134724 | ||
| Structural equilibrium of DNA represented with different force fields | Q34168319 | ||
| DNA polymorphism: a comparison of force fields for nucleic acids | Q34180532 | ||
| Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations | Q34186247 | ||
| Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps | Q34188047 | ||
| Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions | Q34243228 | ||
| Easy DNA modeling and more with GraphiteLifeExplorer | Q34545259 | ||
| Minor groove deformability of DNA: a molecular dynamics free energy simulation study | Q35023850 | ||
| MMPBSA.py: An Efficient Program for End-State Free Energy Calculations | Q35852140 | ||
| A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions | Q36571617 | ||
| Towards a molecular dynamics consensus view of B-DNA flexibility | Q36633176 | ||
| Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution | Q36804416 | ||
| Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). | Q36888664 | ||
| Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent | Q37058615 | ||
| A short guide for molecular dynamics simulations of RNA systems. | Q37302264 | ||
| Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide | Q37486835 | ||
| Frontiers in molecular dynamics simulations of DNA. | Q37914843 | ||
| The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies | Q38052698 | ||
| Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles | Q38389887 | ||
| Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase. | Q38434060 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Evaluation of DNA Force Fields in Implicit Solvation | Q38848165 | ||
| Modelling extreme stretching of DNA. | Q39716585 | ||
| Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations | Q40286618 | ||
| Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald | Q40291611 | ||
| Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. | Q41476736 | ||
| Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations | Q41626260 | ||
| Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions | Q41952799 | ||
| Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations | Q41957783 | ||
| Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. | Q42226830 | ||
| Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters | Q42255582 | ||
| Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility | Q43809888 | ||
| Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution | Q44311276 | ||
| DNA deformation energetics and protein binding | Q44632568 | ||
| Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure | Q44867316 | ||
| Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration | Q46979329 | ||
| Anion binding to nucleic acids | Q47964522 | ||
| Dynamics of B-DNA on the microsecond time scale. | Q50141941 | ||
| Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions. | Q51607649 | ||
| Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. | Q52230498 | ||
| Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. | Q52237592 | ||
| Conformational sub-states in B-DNA. | Q52416199 | ||
| Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. | Q53872406 | ||
| Evaluating nonpolarizable nucleic acid force fields: a systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients. | Q54425622 | ||
| A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules | Q55918670 | ||
| Anton, a special-purpose machine for molecular dynamics simulation | Q56019494 | ||
| THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Q56157177 | ||
| Millisecond-scale molecular dynamics simulations on Anton | Q56224559 | ||
| An improved nucleic acid parameter set for the GROMOS force field | Q56225273 | ||
| Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics Simulations | Q59166694 | ||
| P304 | page(s) | 7.10.1-21 | |
| P577 | publication date | 2014-03-26 | |
| P1433 | published in | Current protocols in nucleic acid chemistry / editorial board, Serge L. Beaucage ... [et al.] | Q26867044 |
| P1476 | title | Molecular modeling of nucleic Acid structure: setup and analysis | |
| P478 | volume | 56 |
| Q89393574 | Deformability Calculation for Estimation of the Relative Stability of Chemically Modified RNA Duplexes | cites work | P2860 |
Search more.