The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Anisotropic network model: systematic evaluation and a new web interface
Open accessAbstract
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 () Contact: bahar@ccbb.pitt.edu
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Yang, L.-W., & Bahar, I. (2005) · Structure · doi:10.1016/j.str.2005.03.015 · Cited by 273
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Cited by
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
Global dynamics of proteins: bridging between structure and function
Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131258 · Cited by 610
Self-citationNormal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
Bahar, I., Lezon, T. R., Bakan, A., & Shrivastava, I. H. (2010) · Chemical Reviews · doi:10.1021/cr900095e · Cited by 537
Self-citationThe Bio3D packages for structural bioinformatics
Grant, B. J., Skjærven, L., & Yao, X. (2021) · Protein Science · doi:10.1002/pro.3923 · Cited by 462
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
Bahar, I., Chennubhotla, C., & Tobi, D. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.09.011 · Cited by 306
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Metadata
- Authors
- Eyal, E., Yang, L.-W., & Bahar, I.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-08-23
- Volume
- 22
- Issue
- 21
- Pages
- 2619-2627
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2113971181
- Cited by
- 322
- References
- 3
- FWCI
- 5.53
- Type
- journal article
- Language
- en
- Open access
- hybrid
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