On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 1999-09, Vol.36 (4), p.419-424 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Amadei, Andrea Ceruso, Marc A. Di Nola, Alfredo |
| description | In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, we obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces, at least within the nanoseconds time range. Proteins 1999;36:419–424. © 1999 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U |
| format | Article |
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| identifier | ISSN: 0887-3585 |
| ispartof | Proteins, structure, function, and bioinformatics, 1999-09, Vol.36 (4), p.419-424 |
| issn | 0887-3585 1097-0134 |
| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Algorithms Bacterial Proteins Computer Simulation conformational fluctuations Cytochrome c Group - chemistry DNA-Binding Proteins - chemistry essential dynamics Kinetics Models, Molecular molecular dynamics Protein Conformation Proteins - chemistry Statistical Distributions Time Factors |
| title | On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations |
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