Additional functionality for registered users:
Mallur S. Madhusudhan
Marc A. Marti-Renom
ModWeb version r185
There are two ModWeb input options:
Personal data for ModWeb calculations are solely collected for dataset identification, when the models are displayed in ModBase, and for interaction with other servers.
If non-standard sequences (i.e. a sequence that is not 100% identical to a
sequence in SwissProt, TrEMBL or Genpept) are submitted in ModWeb,
it is advisable to create the following header line for each sequence
>CU|information about sequence
CU stands for "Custom". In this case, ModBase will display everything following the | in the results table. This makes the identification of input sequences in the ModBase output much easier.
If checked, the model(s) will be added to ModBase's academic dataset, and will be accessible to all academic users. Keep in mind that your dataset name will be displayed. If you're modeling proprietary sequences, please turn this option off.
By default, ModWeb calculates a large number of models and alignments for each input sequence, if a template is available. By default, the models with the highest MPQS and sequence identity per region are selected. To select additional models, check "best scoring model" (best model according to the DOPE score), or "longest well scoring model" (a DOPE score geared to models with higher target coverage).
When the FAST Option is selected for model leverage calculations, ModWeb takes a shortcut. Instead of scanning against the whole PDB95 database, only the input PDB profile is considered. This leads to similar end results. However, some statistics calculations are switched off, resulting in results for MPQS and E-value that are not comparable to the full-database values. The FAST method performs 10-20 times faster.
The "Fold Assignment Methods" option controls the method and amount of sampling done in the alignment space. It determines which methods are used to calculate sequence-structure alignments.
Please consult the ModPipe Manual for detailed information about these hits modes. Since the hits mode handling has changed in the development version of ModPipe, the manual of the latest release doesn't cover the changes especially the newest options (HHBlits and HHSearch). A public release is planned for early 2014.
To use ModWeb, input of the MODELLER license key is required. For further information, please consult http://salilab.org/modeller/registration.html.