Anisotropy of fluctuation dynamics of proteins with an elastic network model.
By A. Atilgan, S. Durell, Robert L. Jernigan, M. Demirel, O. Keskin, Ivet Bahar. Biophysical Journal, 2001
1,524 citations recorded by the source corpus.
Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/4bb72a20e39dc2224d842740e42136a799babe0b
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In Atomic and Molecular Physics, and Optics
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Citations in the corpus
- Coarse-grained models for proteins. (2005, methodology): “elastic networks have also been used together with allatom descriptions [8,10]).”
- Anisotropic network model: systematic evaluation and a new web interface (2006, background): “Eran Eyal, Lee-Wei Yang and Ivet Bahar * Department of Computational Biology, School of Medicine, University of Pittsburgh, PA 15213, USA”
- Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. (2005, methodology): “In the cases of elastic NMA (Atilgan et al., 2001; Hinsen, 1998; Ming et al., 2002a, 2003b; Tama et al., 2002; Tirion, 1996), only the eigenvectors are immediately meaningful.”
- Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, methodology): “These include the popular anisotropic network model (ANM) [19], the associated parameter-free ANM [20], and a more sophisticated C-alpha force field derived from fitting to the Amber94 allatom potential [21].”
- Impact of protein conformational diversity on AlphaFold predictions (2021, methodology): “Temperature factors or B-factors ( B i ) have been obtained performing normal mode analysis (NMA) using the coarse-grained Elastic Network Model [51,52] that considers the protein as an elastic network with nodes linked by springs within a cutoff distance r c .”
- AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening (2019, methodology): “20 In these methods, the diagonalization of the interaction Laplacian matrix is a required procedure to analyze protein fl exibility, which has the computational complexity of (cid:54) N ( ) 3 , with N being the number of matrix elements.”
- Architecture and coevolution of allosteric materials (2016, methodology): “Instead, we use elastic networks, which have been used extensively to describe the vibrational dynamics of proteins [21, 22].”
- Functional dynamics of PDZ binding domains: a normal-mode analysis. (2005, background): “To explore the different role of the PDZ topology with respect to its chemistry in determining the binding movements, we have shifted from the CHARMM force-field, where both topology and full chemical details are taken into account, to the ANM description in its Cβ version, which deals only with the”