
pmid: 17098190
With the increased popularity of normal mode analyses in structural biology, it is important to carefully consider how to best utilize the results for gaining biological insights without over interpretation. The discussion in this article argues that for the purpose of identifying correlated motions in biomolecules, a case separate from concomitant conformational changes of structural motifs, it is generally important to use a large number of normal modes. This is illustrated through three increasingly complex examples. The simplest case includes two bilinearly coupled harmonic oscillators and serves as a straightforward problem where the important considerations are explicit and transparent. The argument is then generalized to include a system of N-coupled harmonic oscillators and finally to a realistic biomolecule. Although a small number of normal modes are useful for probing structural flexibility, it is clear that a much larger number of modes are required for properly investigating correlated motions in biomolecules.
Ions, Models, Molecular, Crystallography, Models, Statistical, Molecular Structure, Protein Conformation, Amino Acid Motifs, Molecular Conformation, Proteins, Ligands, Structural Biology, Oscillometry, Databases, Protein, Molecular Biology, Algorithms, Protein Binding
Ions, Models, Molecular, Crystallography, Models, Statistical, Molecular Structure, Protein Conformation, Amino Acid Motifs, Molecular Conformation, Proteins, Ligands, Structural Biology, Oscillometry, Databases, Protein, Molecular Biology, Algorithms, Protein Binding
| selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 71 | |
| popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network. | Top 10% | |
| influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Top 10% | |
| impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network. | Top 10% |
