iMODS: internal coordinates normal mode analysis server
نویسندگان
چکیده
منابع مشابه
iMODS: 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...
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MOTIVATION Dynamic simulations of systems with biologically relevant sizes and time scales are critical for understanding macromolecular functioning. Coarse-grained representations combined with normal mode analysis (NMA) have been established as an alternative to atomistic simulations. The versatility and efficiency of current approaches normally based on Cartesian coordinates can be greatly e...
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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...
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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...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2014
ISSN: 1362-4962,0305-1048
DOI: 10.1093/nar/gku339