From owner-chemistry@ccl.net Thu Mar 1 07:59:01 2007 From: "Konrad Hinsen hinsen!^!cnrs-orleans.fr" To: CCL Subject: CCL: Question on Gaussian Network Model ! Message-Id: <-33712-070301064015-17279-DkBzKGyYbIR9VGFGLDvn6w~!~server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Thu, 1 Mar 2007 06:40:12 -0500 Sent to CCL by: "Konrad Hinsen" [hinsen]~[cnrs-orleans.fr] On 28.02.2007, at 07:07, Pradipta Bandyopadhyay pradipta:iitg.ernet.in wrote: >Applying GNM to a protein (whose structure is a bit open), I found that in >some regions B-factors obtained from calculation is different from >experimental one (for the rest other regions these are close). This >probably means using one gamma may not be enough. Does anyone know if >there is any simple way to use more than one gamma in GNM (any other >suggestion would be appreciated also)? It is certainly possible to use different gammas for the different interacting pairs, but I am not aware of anyone having done so in a GNM. If you are reasonably sure that the experimental B factors are reliable, then my first suggestion would be to try an elastic network model, i.e. a model taking into account the directions of atomic displacements. This increases the number of coordinates in your system by a factor of three, but that difference matters only for huge proteins. You gain in two points: 1) The description with three coordinates per C-alpha atom is in itself more precise and thus more realistic. 2) The GNM potential is physically unrealistic in not being invariant under rotations. This means that it penalizes global rotations (which you probably don't care about), but also rotational domain motions which you may well have in your protein. There is also a wider choice of potential models that have been published for elastic network models. The most widely used variety of elastic network models uses a force constant that depends on the interatomic distance in the input configuration, nearby atom pairs interacting stronger than more distant ones. In this family we find, in historical order: 1) A exp(-r^2) decrease with distance: K Hinsen Analysis of domain motions by approximate normal mode calculations Proteins 33:417-429 (1998) http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_1998 2) A more complex function obtained from fitting to the Amber94 all-atom potential: K Hinsen, A J Petrescu, S Dellerue, M C Bellissent-Funel, and G R Kneller Harmonicity in slow protein dynamics Chem. Phys. 261(1+2):25-37 (2000) http://dirac.cnrs-orleans.fr/plone/publications/all-publications/Hinsen2000a 3) A step function: constant up to a cutoff distance, then zero (like for GNM): A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model Biophys. J. 80, 505515 (2001) The best model is probably the one described in 2). You can find a ready-to-use implementation in the Molecular Modelling Toolkit (http://dirac.cnrs-orleans.fr/MMTK, it's called CalphaForceField there). There is also a Web server that performs various normal-mode based calculations (including B factors) using this model for any PDB file you submit; the address is http://www.bioinfo.no/tools/normalmodes I remember having seen a paper that modifies the elastic network model in choosing the force constants in a more protein-specific way, but I don't have the reference at hand. Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen+*+cnrs-orleans.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Mar 1 11:43:00 2007 From: "Giulia Caron giulia.caron\a/unito.it" To: CCL Subject: CCL: BIOCUBE Message-Id: <-33713-070301101337-20093-4RlLy+AQbCub5wbwZT6Myw]*[server.ccl.net> X-Original-From: "Giulia Caron" Date: Thu, 1 Mar 2007 10:13:34 -0500 Sent to CCL by: "Giulia Caron" [giulia.caron ~~ unito.it] Hello everybody, BIOCUBE (v.1.0.0) is a free independent computational tool developped by our research group (www.casmedchem.unito.it) that extracts the most relevant information from GRID output files (GRID, Version 22b, Molecular Discovery Ltd). BIOCUBE filters and computes MIFs points with an energy equal to or lower than a given threshold defined by the user, enables their elementary clusterization and allows their visual inspection and manipulation with a wide number of common molecular modelling packages. If you are interested in BIOCUBE, please have a look at http://www.casmedchem.unito.it/pg011.html Best regards Giulia Caron