منابع مشابه
Normalizing normal mode analysis.
Few would disagree, but a generation later, the statement remains a prophecy rather than fact. Although 41,000 protein structures are known, there are none for which there is a complete description of the dynamics that is often key to understanding functional mechanism. Despite keen interest in protein dynamics, studies have remained the purview of computer simulation while the challenges of ex...
متن کاملNormal Mode Analysis Techniques in Structural Biology
The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA) approximates the complex dynamicalbehaviourofa macromoleculeas a simple setof harmonic oscillators vibrating around a given equilibrium conformation. This technique, originated from classical mechanic...
متن کاملInterpreting correlated motions using normal mode analysis.
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, i...
متن کاملiMODS: internal coordinates normal mode analysis server
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends i...
متن کاملInstantaneous normal mode analysis of liquid water
Instantaneous normal mode analysis of orientational motions in liquid water: Local structural effects We present an instantaneous-normal-mode analysis of liquid water at room temperature based on a computer simulated set of liquid configurations and we compare the results to analogous inherent-structure calculations. The separate translational and rotational contributions to each instantaneous ...
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ژورنال
عنوان ژورنال: Structure
سال: 2007
ISSN: 0969-2126
DOI: 10.1016/j.str.2007.01.008