Comparative Models from ModBase

Models of a protein can be fetched by SwissProt, TrEMBL, GenPept or PIR accession code from ModBase using Fetch by ID or the command open (with prefix modbase:). The database contains comparative models created with Modeller, as described in:

ModBase, a database of annotated comparative protein structure models, and associated resources. Pieper U, Webb BM, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74.

The models are not oriented consistently, so it may be helpful to superimpose any that overlap in sequence range. Model starting and ending residue numbers are reported as Target Begin and Target End in the Model List. The command match can be used with specified residue ranges. Alternatively, MatchMaker (or its command equivalent, mmaker) can be used: it does not require specifying residue numbers, but is not as fast as match.

See also: Chimera interface to Modeller

Each row in the dialog describes a model protein structure. Besides models from ModBase, this Model List dialog is also used to show the results of running Modeller from Chimera. Each type of information [details at ModBase] can be shown or hidden using the Columns menu. Not all values are available for all models. The Model List is included in saved sessions.

The Fetch Scores menu allows using the SaliLab Model Evaluation Server to fill in certain scores for any models lacking them: zDOPE, Estimated RMSD, and Estimated Overlap (3.5 Å). The evaluation server requires a Modeller license key, provided upon free registration to academic users.

• Model - model ID number in Chimera
• GA341 - model score derived from statistical potentials (see Melo et al., Protein Sci 11:430 (2002)); automatically assigned as a model attribute named modScore_GA341. A value > 0.7 generally indicates a reliable model, defined as ≥ 95% probability of correct fold.
• ModPipe Quality Score - composite model score based on sequence identity, template coverage, E-value, zDOPE, and GA341; automatically assigned as a model attribute named modScore_MPQS. A value > 1.1 generally indicates a reliable model.
• zDOPE - normalized Discrete Optimized Protein Energy (DOPE), an atomic distance-dependent statistical score (see Shen and Sali, Protein Sci 15:2507 (2006)); automatically assigned as a model attribute named modScore_zDOPE. Negative values indicate better models. Missing values can be added with Fetch Scores.
• Estimated RMSD - TSVMod-predicted Cα root-mean-square deviation (RMSD) of the model from the native structure (see Eramian et al., Protein Sci 17:1881 (2008)); automatically assigned as a model attribute named modScore_estRMSD. Missing values can be added with Fetch Scores.
• Estimated Overlap (3.5 Å) - TSVMod-predicted native overlap (3.5 Å), fraction of Cα atoms in the model within 3.5 Å of the corresponding atoms in the native structure after rigid-body superposition (see Eramian et al., Protein Sci 17:1881 (2008)); automatically assigned as a model attribute named modScore_estOverlap. Missing values can be added with Fetch Scores.
• Sequence Identity - percent sequence identity between target and template reported by template search; automatically assigned as a model attribute named modbaseSequenceIdentity
• E-value - significance of target-template sequence alignment reported by template search (not the modeling alignment); automatically assigned as a model attribute named modbaseEvalue
• Template PDB - PDB ID of template structure
• Template Chain - chain ID of template structure
• Template Begin - starting residue of region used as template
• Template End - ending residue of region used as template
• Target Length - length of target sequence (not model)
• Target Begin - starting residue of model
• Target End - ending residue of model
• ModPipe Run - ModBase dataset
• ModPipe Model Id - database identifier for model
• ModPipe Alignment Id - database identifier for sequence alignment
• Program - ModPipe version
• Experiment Type - THEORETICAL MODEL
• Method - HOMOLOGY MODELING

The model list can be sorted by the values in any displayed column by clicking the column header. Clicking the header once sorts the entries in order of increasing value and places an up arrowhead (triangle) in the header. Clicking again sorts the entries in decreasing order and places a down arrowhead (inverted triangle) in the header.

A model can be chosen by clicking on its line, and multiple models can be chosen at once. Chosen lines are highlighted in the dialog. Ctrl-click toggles the status of a line, while clicking on the first (or last) line of a contiguous block and then Shift-clicking on the last (or first) chooses all of the lines in the block.

Clicking the black arrowhead reveals/hides options for the Treatment of Chosen Models:

• Select atoms - select all atoms in the models
• Choose in Model Panel - also choose the models in the Model Panel for further operations, such as:
  • match... open the MatchMaker tool to superimpose structures. Of course, only models that overlap in sequence range are expected to superimpose. Model start and end residue numbers are reported as Target Begin and Target End in the model list.
  • focus - center the display on the chosen model(s)
  • rainbow... color the chosen model(s) over a range with the Rainbow tool
  • render/sel by attr... open the Render/Select by Attribute tool, for example to color by bfactor (actually the Modeller error profile in these models) or to show modbaseModelScore with worm thickness
  • show only - show the chosen model(s) and hide all of the others
  • write PDB - bring up a dialog for saving models as PDB files
  In most further dialogs opened from the Model Panel, the same models will be chosen automatically.
• Hide others - hide the other models in the model list

Hide hides the dialog without removing it; Quit removes the dialog and closes the structures. Help brings up this manual page in a browser window.