Analysis of the relative contributions of the nuclear Overhauser interproton distance restraints and the empirical energy function in the calculation of oligonucleotide structures using restrained molecular dynamics

Biochemistry ◽  
1989 ◽  
Vol 28 (14) ◽  
pp. 5978-5984 ◽  
Author(s):  
Angela M. Gronenborn ◽  
G. Marius Clore
Keyword(s):  
Molecular Dynamics ◽  
Energy Function ◽  
Interproton Distance ◽  
Distance Restraints ◽  
Nuclear Overhauser ◽  
Restrained Molecular Dynamics

Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G)2

1986 ◽  
Vol 188 (3) ◽  
pp. 455-475 ◽  
Author(s):  
Lennart Nilsson ◽  
G.Marius Clore ◽  
Angela M. Gronenborn ◽  
Axel T. Brünger ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Overhauser Effect ◽  
Structure Refinement ◽  
Interproton Distance ◽  
Overhauser Effect ◽  
Distance Restraints ◽  
Nuclear Overhauser

Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination

1986 ◽  
Vol 191 (3) ◽  
pp. 523-551 ◽  
Author(s):  
G.Marius Clore ◽  
Axel T. Brünger ◽  
Martin Karplus ◽  
Angela M. Gronenborn
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Structure Determination ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Interproton Distance ◽  
Distance Restraints

scholarly journals Determination of the backbone conformation of secretin by restrained molecular dynamics on the basis of interproton distance data

1988 ◽  
Vol 171 (3) ◽  
pp. 479-484 ◽  
Author(s):  
G. Marius CLORE ◽  
Michael NILGES ◽  
Axel BRUNGER ◽  
Angela M. GRONENBORN
Keyword(s):  
Molecular Dynamics ◽  
Interproton Distance ◽  
Backbone Conformation ◽  
Distance Data ◽  
Restrained Molecular Dynamics

Practical applications of time-averaged restrained molecular dynamics to ligand-receptor systems: FK506 bound to the Q50R,A95H,K98I triple mutant of FKBP-13

1996 ◽  
Vol 8 (1) ◽  
Author(s):  
ChristopherA. Lepre ◽  
DavidA. Pearlman ◽  
Olga Futer ◽  
DavidJ. Livingston ◽  
JonathanM. Moore
Keyword(s):  
Molecular Dynamics ◽  
Triple Mutant ◽  
Practical Applications ◽  
Restrained Molecular Dynamics

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Time-averaged nuclear overhauser effect distance restraints applied to tendamistat

1990 ◽  
Vol 214 (1) ◽  
pp. 223-235 ◽  
Author(s):  
Andrew E. Torda ◽  
Ruud M. Scheek ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Nuclear Overhauser Effect ◽  
Overhauser Effect ◽  
Distance Restraints ◽  
Nuclear Overhauser
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