Calibrating nucleic acids torsional energetics in force-field: insights from model compounds (Q57901407)

5

0 references

author name string

D Bosch

1

0 references

N Foloppe

2

0 references

L Pardo

Computational and Theoretical Chemistry

4

0 references

publication date

March 2001

0 references

published in

0 references

volume

537

0 references

issue

1-3

0 references

page(s)

283-305

0 references

cites work

BI-BII transitions in B-DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

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).

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Conformational properties of the TATA-box binding sequence of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Crystallographic water sites from a theoretical perspective

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Rules governing the orientation of the 2'-hydroxyl group in RNA

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Selective binding of the TATA box-binding protein to the TATA box-containing promoter: analysis of structural and energetic factors

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Structural equilibrium of DNA represented with different force fields

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

New insights into sequence-dependent DNA structure

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

The B-DNA dodecamer at high resolution reveals a spine of water on sodium

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

The conformation of the DNA double helix in the crystal is dependent on its environment

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

"...the tyranny of the lattice...".

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics.

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Comparison of the crystal and solution structures of two RNA oligonucleotides

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm an

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

How accurately and precisely can RNA structure be determined by NMR?

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

The structure of a stable intermediate in the A left-right-arrow B DNA helix transition

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

C-H...O hydrogen bonding in biology

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

RNA hydration: a detailed look

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

The orientation and dynamics of the C2'-OH and hydration of RNA and DNA.RNA hybrids

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator

1 reference

https://api.crossref.org/works/10.1016%2FS0166-1280%2800%2900685-0

7 January 2021

Crystallographic evidence for the existence of CH...O, CH...N and CH...Cl hydrogen bonds

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1021/JA00383A012