the spring characteristics. Furthermore, the results from the network model can be scaled up to obtain the structural response at the macroscale using FE analysis. Decomposition of flexible/rigid regions and domains of proteins Characterization of functional motions and functionally important sites/residues of proteins, enzymes and large macromolecular assemblies Refinement and dynamics of low-resolution structural data, e.g. Cryo-electron microscopy Molecular replacement for solving X-ray structures, when a conformational change occurred, with respect to a known structure Integration with atomistic models and simulations Investigation of folding/unfolding pathways and kinetics. Annotation of functional implication in molecular evolution Web servers In practice, two kinds of calculations can be performed. The first kind (the GNM per se) makes use of the Kirchhoff matrix. The second kind (more specifically called either the Elastic Network Model or the Anisotropic Network Model) makes use of the Hessian matrix associated to the corresponding set of harmonic springs. Both kinds of models can be used online, using the following servers. GNM servers iGNM: A database of protein functional motions based on GNM http://ignm.ccbb.pitt.edu oGNM: Online calculation of structural dynamics using GNM https://web.archive.org/web/20070516042756/http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm ENM/ANM servers Anisotropic Network Model web server http://www.ccbb.pitt.edu/anm elNemo: Web-interface to The Elastic Network Model http://www.sciences.univ-nantes.fr/elnemo/ AD-ENM: Analysis of Dynamics of an Elastic Network Model http://enm.lobos.nih.gov/ WEBnm@: Web-server for Normal Mode Analysis of proteins http://apps.cbu.uib.no/webnma/home Other relevant servers ProDy: An Application Programming Interface (API) in Python, that integrates GNM and ANM analyses and several molecular structure and sequence analyses and visualization tools: http://prody.csb.pitt.edu HingeProt: An algorithm for protein hinge prediction using elastic network models http://www.prc.boun.edu.tr/appserv/prc/hingeprot/, or http://bioinfo3d.cs.tau.ac.il/HingeProt/hingeprot.html DNABindProt: A Server for Determination of Potential DNA Binding Sites of Proteins http://www.prc.boun.edu.tr/appserv/prc/dnabindprot/ MolMovDB: A database of macromolecular motions: http://www.molmovdb.org/ See also Gaussian distribution Harmonic oscillator Hooke's law Molecular dynamics Normal mode Principal component analysis Protein dynamics Rubber elasticity Statistical mechanics References Primary sources Cui Q, Bahar I, (2006). Normal Mode Analysis: Theory and applications to biological and chemical systems, Chapman & Hall/CRC, London, UK Specific citations Molecular modelling