Calculations of nucleic acid conformations (Q41110010)

26 September 2017

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title

Calculations of nucleic acid conformations (English)

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26 September 2017

Louise-May S

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26 September 2017

Auffinger P

series ordinal

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26 September 2017

Westhof E

series ordinal

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26 September 2017

publication date

1 June 1996

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Current Opinion in Structural Biology

26 September 2017

published in

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26 September 2017

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26 September 2017

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26 September 2017

page(s)

289-298

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Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases.

26 September 2017

cites work

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7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

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7 January 2021

H-Bonded and Stacked DNA Base Pairs: Cytosine Dimer. An Ab Initio Second-Order Moeller-Plesset Study

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Contributions of the thymine methyl group to the specific recognition of poly- and mononucleotides: an analysis of the relative free energies of solvation of thymine and uracil.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Modelling DNA conformational mechanics

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Measuring the geometry of DNA grooves.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular dynamics simulations of the effects of ring‐saturated thymine lesions on DNA structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular modelling study of DNA-Troeger's bases interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular Dynamics Study of the Binding of Elsamicin A to DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Theoretical studies of DNA-RNA hybrid conformations.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular Dynamics Simulations of a r(GA12G)·d(CT12C) Hybrid Duplex

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Symmetry and structure of RNA and DNA triple helices.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Structural polymorphism in d(T)12.d(A)12*d(T)12 triple helices

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Solvent effects on model d(CG.G)7 and d(TA.T)7 DNA triple helices

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G4TnG4)

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Structural properties of the [d(G3T4G3)]2 quadruplex: evidence for sequential syn-syn deoxyguanosines

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Rigid-Body Motions of Sub-Units in DNA: A Correlation Analysis of a 200 ps Molecular Dynamics Simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Conformational transitions using molecular dynamics with minimum biasing.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Dynamics of transfer RNAs analyzed by normal mode calculation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

"Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

A genetic algorithm to search for optimal and suboptimal RNA secondary structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The computer simulation of RNA folding pathways using a genetic algorithm.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints

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https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Statistics of RNA melting kinetics.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Diversity of oligonucleotide functions

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https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The Structure of Ribosomal RNA: A Three-Dimensional Jigsaw Puzzle

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

A genetic algorithm based molecular modeling technique for RNA stem-loop structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

B-DNA twisting correlates with base-pair morphology.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The construction of DNA helical duplexes along prescribed 3-D curves.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Configurational statistics of the DNA duplex: extended generator matrices to treat the rotations and translations of adjacent residues

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

On higher buckling transitions in supercoiled DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

The influence of salt on the structure and energetics of supercoiled DNA

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https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions

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https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

A smooth particle mesh Ewald method

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980046-7

7 January 2021

10.1016/S0959-440X(96)80046-7

Identifiers

DOI

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26 September 2017

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