ModWeb Help Pages

Server availability

The ModWeb server is freely available to all academic users. The server administrators reserve the right to rate-limit or delete jobs to keep the service running for all if it is abused (e.g. submitting hundreds of jobs). (For bulk jobs, download MODELLER and run locally.)

ModWeb Input Mode

There are two ModWeb input options:

• Single or Multiple Sequences:
  Multiple Sequences (up to 100) can be pasted into the textfield or a FASTA file can be uploaded. Please note the header specifications for easier viewing of the results.
• Model leverage:
  The given PDB chain is used as a template to calculate models of all sequences in SwissProt/TrEMBL that are related to this template structure. (Note that if you want to build a model of a given sequence using your own choice of template, this is not what you want. Download Modeller and use that instead.) This option is currently in the test phase, and is only available to registered users.

ModWeb General Information

Personal data for ModWeb calculations are solely collected for dataset identification, when the models are displayed in ModBase, and for interaction with other servers.

ModWeb FASTA Format

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.

Availability (academic dataset)

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.

ModWeb Model Selection

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).

ModWeb Template FAST Option

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.

ModWeb Fold Assignment Methods

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.

• Very Fast (Seq-Seq): pairwise sequence alignments to calculate alignments
• Fast (Seq-Prf): sequence-sequence and sequence-profile methods (Modeller Build-Profile)
• Slow (Seq-Prf, PSI-Blast): the above methods plus PSI-Blast
• Very Slow (Slow + Build-Profile): includes all of the methods above and also adds profile-profile alignment methods from Modeller
• HHBlits (test-mode): Seq-Seq and HHBlits profile methods.
• HHSearch (test-mode): Seq-Seq, HHBlits, and HHSearch profile methods.

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.

Modeller License Key

To use ModWeb, input of the MODELLER license key is required. For further information, please consult the MODELLER registration page.