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Andrew E. Torda
Researcher at University of Hamburg
Publications - 86
Citations - 5204
Andrew E. Torda is an academic researcher from University of Hamburg. The author has contributed to research in topics: Threading (protein sequence) & Protein structure. The author has an hindex of 27, co-authored 84 publications receiving 4973 citations. Previous affiliations of Andrew E. Torda include Australian National University & University of New South Wales.
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Journal ArticleDOI
The GROMOS Biomolecular Simulation Program Package
Walter R. P. Scott,Philippe H. Hünenberger,Ilario G. Tironi,Alan E. Mark,S. R. Billeter,Jens Fennen,Andrew E. Torda,Thomas Huber,Peter Kruger,W. F. van Gunsteren +9 more
TL;DR: The newest version of the GROningen MOlecular Simulation program package, GROMOS96, has been developed for the dynamic modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism.
Journal Article
The GROMOS biomolecular simulation program package
Walter R. P. Scott,Philippe H. Hünenberger,Ilario G. Tironi,Alan E. Mark,S. R. Billeter,Jens Fennen,Andrew E. Torda,Peter Kruger,W. F. van Gunsteren,Thomas Huber +9 more
TL;DR: The GROningen MOlecular Simulation (GROMOS) program package as mentioned in this paper has been developed for the dynamic modeling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism.
Journal ArticleDOI
Local elevation: A method for improving the searching properties of molecular dynamics simulation
TL;DR: Although the concept of memory has been introduced into a molecular dynamics algorithm, it can only be applied to systems with a small number of degrees of freedom, and offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few.
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Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.
TL;DR: The molecular dynamics simulations show that the time-averaged constraints increase the mobility allowed to molecules, produce better agreement with distance bounds, improve searching properties and give a better estimate of the conformational space occupied by the molecule in solution.
Journal ArticleDOI
Time-dependent distance restraints in molecular dynamics simulations
TL;DR: In this article, a method for enforcing nuclear Overhauser effect (NOE) distance restraints in molecular dynamics simulations is presented, in which a term is included in the force field such that the distance restraint need only be satisfied as a ǫ r −3 −1/3 weighted time average over the simulation trajectory.