Anisotropic network model: systematic evaluation and a new web interface
By Eran Eyal, Lee-Wei Yang, Ivet Bahar. Bioinform., 2006
326 citations recorded by the source corpus.
MOTIVATION The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage. RESULTS ANM has been evaluated on a large set of proteins to establish the optimal model parameters that achieve the highest correlation with experimental data and its limits of accuracy and applicability. Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones. Significant improvement in agreement with experiments is observed with increase in the resolution of the examined structure. A new server for ANM calculations is presented, which offers flexible options for controlling model parameters and output formats, interactive animation of collective modes and advanced graphical features. AVAILABILITY ANM server (http://www.ccbb.pitt.edu/anm)
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/60779faf5282abdc9b6c11da48dbeec17cae7fad
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In Materials Chemistry
- Xin-Qiu Yao
- Barry J. Grant
- Lars Skjaerven
- Timothy R. Lezon
- Ivet Bahar
- Lars Skjærven
- Eran Eyal
- Lee-Wei Yang
In Molecular Biology
- Xin-Qiu Yao
- Barry J. Grant
- Lars Skjaerven
- Eran Eyal
- Lee-Wei Yang
- Timothy R. Lezon
- Ivet Bahar
- Lars Skjærven
Citations in the corpus
- The Bio3D packages for structural bioinformatics (2020, methodology): “A number of previously implemented software solutions (including multiple web servers 31 – 35 and standalone software packages 36 – 42 ) offer related solutions including single structure NMA, MD or protein structure-based network analysis.”
- Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, background): “As noted in the introduction, a number of previously implemented software solutions (including multiple web-servers [10-12,45] and standalone software packages [13-15,46]) offer single structure NMA or MD analysis.”
- Global dynamics of proteins: bridging between structure and function. (2010, methodology): “60 upon consideration of crystal contacts (21); the use of distance-weighted spring constants further increases the average correlation with experimental B-factors to 0.”