oGNM: online computation of structural dynamics using the Gaussian Network Model.

Lee-Wei Yang; A J Rader; Xiong Liu; Cristopher Jon Jursa; Shann Ching Chen; Hassan A Karimi; Ivet Bahar

doi:10.1093/nar/gkl084

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oGNM: online computation of structural dynamics using the Gaussian Network Model.

Lee-Wei Yang·A J Rader·Xiong Liu·Cristopher Jon Jursa·Shann Ching Chen·Hassan A Karimi·Ivet Bahar

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Abstract

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5-6 orders of magnitude faster than those using conventional normal mode analyses. Two cases studies illustrate the utility of oGNM. The first shows that the thermal fluctuations predicted for 1250 non-homologous proteins correlate well with X-ray crystallographic data over a broad range [7.3-15 A] of inter-residue interaction cutoff distances and the correlations improve with increasing observation temperatures. The second study, focused on 64 oligonucleotides and oligonucleotide-protein complexes, shows that good agreement with experiments is achieved by representing each nucleotide by three GNM nodes (as opposed to one-node-per-residue in proteins) along with uniform interaction ranges for all components of the complexes. These results open the way to a rapid assessment of the dynamics of DNA/RNA-containing complexes. The server can be accessed at http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm.

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Algorithms Computational Biology Computer Graphics Databases, Protein Internet Models, Statistical Motion Normal Distribution Nucleic Acid Conformation Oligonucleotides Protein Conformation Proteins Software User-Computer Interface Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

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Lee-Wei Yang, A J Rader, Xiong Liu, Cristopher Jon Jursa, Shann Ching Chen, Hassan A Karimi, Ivet Bahar. 2006-07-01. oGNM: online computation of structural dynamics using the Gaussian Network Model.. https://doi.org/10.1093/nar%2Fgkl084

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