Coarse-grained normal mode analysis in structural biology.
By Ivet Bahar, A. Rader. Current Opinion in Structural Biology, 2005
717 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology, Structural Biology
View Paper: https://www.semanticscholar.org/paper/4abee5a867c4abb97e4de80a1b339b20fb120e46
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Erik Lindahl
- Patrice Koehl
- Cyril Azuara
- José Ramón López-Blanco
- Pablo Chacón
- Gustavo D. Parisi
- Marc Delarue
- Tadeo E. Saldaño
In Molecular Biology
- Patrice Koehl
- Cyril Azuara
- Erik Lindahl
- Jean-Pierre Changeux
- José Ramón López-Blanco
- Pablo Chacón
- Gustavo D. Parisi
- Marc Delarue
In Structural Biology
- José Ramón López-Blanco
- Erik Lindahl
- Patrice Koehl
- Pablo Chacón
- Cyril Azuara
- Marc Delarue
- José Ignacio Garzón
Citations in the corpus
- iMod: multipurpose normal mode analysis in internal coordinates (2011, positive): “Normal mode analysis (NMA) merged with coarse-grained (CG) models has proven to be a powerful and popular alternative to simulate collective motions of macromolecular complexes at extended timescales (Bahar and Rader, 2005; Bahar et al., 2010; Cui and Bahar, 2007; Ma, 2005; Skjaerven et al., 2009; T”
- Protein-protein docking with backbone flexibility. (2007, neutral): “include molecular dynamic simulations in combinationwith principal components analysis,(41) analysis of variations in homologous structures in a protein family, flexibility predictions fromgraph theory(42) and normal mode analysis.(43) In the case of our successful prediction for CAPRI target 20, th”
- Evolutionary Conserved Positions Define Protein Conformational Diversity (2016, background): “A number of previous studies have shown that ligand-associated conformational changes are dominated by only a few low-frequency normal modes[35,50,59,60,61].”
- NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis (2006, methodology): “The striking simplicity of this method has made it quite popular (14,15).”
- Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system (2009, methodology): “Normal-mode analysis (NMA) gives an in silico decomposition of protein movements into discrete modes (the concerted motion of a set of atoms), which may be used to describe the slow (biologically relevant) transitions of protein”
- Docking and scoring protein complexes: CAPRI 3rd Edition (2007, neutral): “24”