What's new in the new version?

  • Inclusion of Nucleic acids in the model. By default every nucleotide is modeled by three nodes: P in the phosphate group, C4' in the base and C2 in the sugar ring. By doing so, nucleic acid network nodes would have comparable spatial density with that of C-alpha.

  • Option for inclusion of ligands in the model. Ligands atoms are now parsed and suggested (although not by default) to be included in the model. The user then need to determine manually the cutoff distance for each such non-standard ligand node.

  • Flexibility in definition of system nodes. While the default nodes are selected as explained above (single Calpha node per amino acid and three nodes per nucleic acid), in this version the user can change these definitions and/or to change the number of nodes per amino/nucleic acid.

  • Flexibility and specificity in cutoff distances. Variable cutoff distance to determine interaction in the Hessian matrix (Gaussian spring) can be set to each atom type. To support this system, the actual threshold distance is a function of the atom pairs and is set to the sum of the specific cutoff distances in each pair of atoms under consideration.

  • New server. We are now using a new Linux server with 128 GB RAM, dedicated to web applications.

  • New software version. All major software applied in this site were now upgraded to latest versions. This includes:
    Matlab: version R2014a
    Jmol: version 13.0.16
    Raster3D: version 3.02
    Perl: version 5.18

  • New eigen solver. Matlab is now applied as the default eigen-solver (eigs function) for calculation of subset of normal modes, as well as to the parts which require calculation of all modes. This allows now the user to define how many modes to calculate. The default is still calculation of the slowest 20 modes. More modes can be calculated if needed. On the other hand, for larger systems, fewer modes can be requested to improve speed and performance. Blzpack can still be selected as an eigensolver as additional option.

  • Easy option to take screen snapshot. Thanks to Jmol developers there is now an easy option implemented in the Jmol page to take screen snapshot images and save them locally.

  • Atomic Displacement Parameters. Again thanks to the Jmol development team, it is now possible to view the anisotropic displacement parameters (ADP) predicted by ANM as ellipsoids inside interactive Jmol session. In the old version, only static images of the ellipsoids was provided. Such images, produced by programs from the Raster3D package can still be obtained, as well as PDB files which includes ANISOU records for atomic displacement parameters.

  • Submit and analyze user defined normal modes. You can calculate normal modes for your molecule elsewhere with other tools and upload them to the server for visualization purposes

  • More convenient interface. For example, for easy navigation in the correlation and distance variation analyses maps.

  • The source code was improved and a package to include ligands in the calculation was added to the source distribution.