Results 1 - 10 of 26,390

VISUALIZING AND IDENTIFYING CONFORMATIONAL ENSEMBLES IN MOLECULAR DYNAMICS TRAJECTORIES

by D Ynamics, Christoph Best
"... Using a conformational distance measure based on the changes in intramolecular atom distances, the authors show that a planar map can help visualize molecular dynamics trajectories efficiently such that conformational ensembles appear as well-separated point sets. Cluster analysis can then be used t ..."
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Using a conformational distance measure based on the changes in intramolecular atom distances, the authors show that a planar map can help visualize molecular dynamics trajectories efficiently such that conformational ensembles appear as well-separated point sets. Cluster analysis can then be used

Instabilities and Non-Reversibility of Molecular Dynamics Trajectories

by R. G. Edwards, Ivan Horváth, A. D. Kennedy , 1996
"... The theoretical justification of the Hybrid Monte Carlo algorithm depends upon the molecular dynamics trajectories within it being exactly reversible. If computations were carried out with exact arithmetic then it would be easy to ensure such reversibility, but the use of approximate floating point ..."
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The theoretical justification of the Hybrid Monte Carlo algorithm depends upon the molecular dynamics trajectories within it being exactly reversible. If computations were carried out with exact arithmetic then it would be easy to ensure such reversibility, but the use of approximate floating point

Abstract VRML Molecular Dynamics Trajectories

by Geoff Leach
"... www.cs.rmit.edu.au/˜gl/ One application of VRML is visualisation of scientific data. Using VRML results of simulations and other scientific endeavours can be published on the web with all the advantages (and disadvantages) the web offers, but with the further advantage that the results are in the fo ..."
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are in the form of interactive, moving 3D “worlds”. This is especially advantageous when the data itself is 3D. In this paper we discuss the use of VRML to publish the results of molecular dynamics simulations on the web. We also discuss a framework for application-specific compression of VRML files which allows

1 Non-Reversibility of Molecular Dynamics Trajectories

by R. G. Edwards, Ivan Horváth, A. D. Kennedy A , 1996
"... We study the non-reversibility of molecular dynamics trajectories arising from the amplification of rounding errors. We analyse the causes of such behaviour and give arguments, indicating that this does not pose a significant problem for Hybrid Monte Carlo computations. We present data for pure SU(3 ..."
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We study the non-reversibility of molecular dynamics trajectories arising from the amplification of rounding errors. We analyse the causes of such behaviour and give arguments, indicating that this does not pose a significant problem for Hybrid Monte Carlo computations. We present data for pure SU

Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories

by Christoph Best, Hans-christian Hege - Computers in Science and Engineering , 2002
"... Simulating the dynamics of complex biomolecules produces trajectories comprising a large number of different configurations of the molecule. These configurations must be classified into a small number of conformational ensembles representing essential changes in the shape of the molecule. Using a co ..."
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Simulating the dynamics of complex biomolecules produces trajectories comprising a large number of different configurations of the molecule. These configurations must be classified into a small number of conformational ensembles representing essential changes in the shape of the molecule. Using a

of molecular dynamics trajectories by Self-Organising Maps

by Fraccalvieri Et Al, Functional Analysis, Domenico Fraccalvieri, Ro P, Fabio Stella, Laura Bonati
"... Self- ..."
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Research Article Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

by Renata De Paris, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto De Souza, Rodrigo C. Barros , 2015
"... Copyright © 2015 Renata De Paris et al.This is an open access article distributed under the Creative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular dynamics simulations of protein recep ..."
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receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context

Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories

by Klara Kedem , Paul Chew , Ron Elber - Proteins , 1999
"... Abstract The Unit-vector RMS (URMS) is a new technique to compare protein chains and to detect similarities of chain segments. It has a number of unique features that include exceptionally weak dependence on the length of the chain and efficient detection of substructure similarities. Two molecular ..."
Abstract - Cited by 23 (2 self) - Add to MetaCart
molecular dynamics simulations of proteins in the neighborhood of their native states are used to test the performance of the URMS. The first simulation is of a solvated myoglobin and the second is of the protein MHC. In accord with previous studies the secondary structure elements (helices or sheets

Root mean square deviation probability analysis of molecular dynamics trajectories on

by Surjit B. Dixit, Sergei Y. Ponomarev, David L. Beveridge , 2006
"... The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed as the representa ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed

Local dielectric environment of B-DNA in solution: Result from a 14 ns molecular dynamics trajectory

by M. A. Young, B. Jayaram, D. L. Beveridge - J. Phys. Chem., B 1998
"... The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood-Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a medium of explicit waters and sodium counterions with particle mesh Ewald for long-range electrostatics. The computed dielectric pro ..."
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The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood-Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a medium of explicit waters and sodium counterions with particle mesh Ewald for long-range electrostatics. The computed dielectric
Results 1 - 10 of 26,390