Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.

By Jianpeng Ma. Structure, 2005

477 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Persistent homology analysis of protein structure, flexibility and folding (2014, methodology): “A more detailed description is available from review literature [75–78].”
Global dynamics of proteins: bridging between structure and function. (2010, background): “, by the fold of the protein), as recently reviewed (5, 50, 65, 76).”
Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective (2012, background): “The advantages and the limitations of this approach has been reviewed [401, 402].”
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures (2018, methodology): “Other computational tools use normal mode analysis (NMA) or various kinds of coarsegrained models (10-14) Their limitations depend on their particular design, especially on the simplifications assumed, and on the modeled system (for example NMA is well suited only for certain systems(15)).”
Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. (2009, unknown): “, Marrink, S-J., & Ceruso, M. A. (2009). Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition.”