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Build Homology Model Panel |
In this panel you can set options for building a homology model and start the job to build the model.
To open the Build Homology Model panel, you can:
Choose Tools → Build Homology Model in the Multiple Sequence Viewer panel.
Click the Build Homology Model button on the Build toolbar of the Multiple Sequence Viewer panel.
If you don't already have a query sequence, an alignment, and structures for the templates, you can use the three buttons at the top of the panel to perform these tasks. Clicking these three buttons in turn performs the most basic homology modeling tasks. However, you might want to adjust the alignment before proceeding to build the model, which you can do in the main panel.
Import Sequence—Import the query sequence as a new query. Opens the Import Sequence dialog box, so you can locate and import the sequence.
Find Templates—Run a BLAST search to identify potential templates. Opens the Blast Search Settings dialog box, to make settings and run the job.
Get Structures—Import structures from the PDB for the current templates.
These options are used to select the kind of model that is built: a single chain model from a single template, from selected regions of multiple templates, or from a consensus of multiple templates; a homo-multimer model; or a hetero-multimer model. The templates must have PDB structures associated with them before you build the model. If any of the templates do not have PDB structures, you must import the structures.
Select this option to build a model for a single chain from a single template. The template must be selected from the available sequences in the MSV, and must have a PDB structure imported.
To build a model for a single chain that makes use of several templates, each in a different region of the query, select this option. To select the regions from each template, drag over the residues that you want to use in the template. When you select this option, the sequence section is outlined in red and the color scheme is removed. The residues used for each region are marked with a different color for each template. The templates that are used are the ones in which you select residues. By default, all residues in the first template are selected, but you can select all residues in another template by clicking the template name.
Select this option to build a homo-multimer. Each template chain must be aligned to the query, and you must select all of the chains that you want to use to build the model. The structures for each template chain must be in the correct relative orientation and location to build the multimer. This usually means that the template will itself be a homo-multimer, but it could also be a hetero-multimer with a high sequence identity between the chains. You can align the chains of the template using multiple sequence alignment, or separately with Align and Merge. If the template is a heteromultimer, you could also build the homomultimer as if it was a heteromultimer.
Select this option to build a model that is a consensus of several templates. Each alpha carbon is placed at the position where the largest number of templates places that carbon. The template structures must be prealigned.
Select this option if you want to build a hetero-multimer model. The Hetero-multimer tab is displayed, so you can select the queries and templates for the multimer. You must do the alignment for each query before you select the queries as templates for the multimer.
Choose the method for building the model in this tab, from the following two methods:
Knowledge-based—Construct insertions and close gaps using segments from known structures. With this option, you can choose to return multiple models of the structure. By default, only one is returned. The models are approximately ordered by the sequence identity and the incidende of clashes in the structure.
Energy-based—Construct and refine residues that do not come from the template based on the energy, including building through structural discontinuities and optimizing side chains.
This tab contains a number of settings for building structures.
Number the residues in the built structure the same as in the template, as far as possible. Does no apply to consensus modeling. When using multiple templates for a single chain, the residue numbers are taken from the first template. Sequential numbering from 1 is used if the attempt to use template numbering fails.
Retain the the rotamers for the side chains of conserved residues. These side chains will not be optimized. This option is selected by default.
Optimize side chains, except for those attached to conserved residues if Retain rotamers for conserved residues is selected. This option is selected by default.
If side chains are optimized, also optimize the residues whose structure is not derived from any of the templates. This option is selected by default.
If there is an insertion in the query (a template gap) that requires the building of a loop, build the loop if it doesn't have more than the specified number of residues, otherwise cut the query sequence and cap it with NMA and ACE. When the template that spans the insertion is cut to build the query, the template residue on the high side of the cut (higher residue number) is also deleted, so that the capping does not result in steric clashes. Cutting could be useful where there are long insertions that are not in the region of interest. The query chain retains its name, regardless of the cuts. The option is selected by default, with a length of 20. If it is not selected, all loops are built.
If there is a junction between two templates, close it if this option is selected, otherwise cap the ends of the two pieces with NMA and ACE. This option is selected by default.
Deletions and Template Junctions—If there are deletions in the query (a query gap), join the pieces of the template when building the structure if this option is selected, otherwise cap the ends of the two pieces with NMA and ACE. This option is selected by default.
In this tab you can select ligands to include in the final model. The available ligands are listed, and you can select ligands from this list. By default, only the ligands and cofactors within 5 Å of the chain used for the template are included in the list. To display the full list, select Show All.
To set proximity constraints on the ligand, click in the empty annotation row for the ligand, which is below the query row, at the position that you want to add a constraint between that residue and the ligand. It might be useful to show ligand contacts for the template, to provide some guidance on where to place the ligand constraints on the query. (This annotation is only displayed when the Ligands tab is active; it is not displayed at the same time as the protein-protein proximity constraints annotation.)
In this tab you can create proximity constraints for pairs of residues. At least one of the residues must be in a loop, since helices and strands do not have the flexibility to adjust to the constraint. A harmonic constraint is added for the terminal heavy atoms of the side chains. If you specify a pair of CYS residues, a disulfide bond is formed.
To set a constraint, select the two residues that you want to be in contact. The constraints are marked in an annotation row with a red curve between the residues. To remove a constraint, select the two residues that are constrained.
In this tab you can select the queries used for each unit of the heteromultimer. The queries are listed by the tab name in the Multiple Sequence Viewer panel. Only those queries that have been set up for model building in the Build Homology Model panel are listed.
To add a query to the list, you must first import it as a new query, find a template and align it in the Multiple Sequence Viewer panel, then open the Build Homology Model panel, select the appropriate option for building the model (single chain, composite, or homo-multimer; consensus cannot be used), and select the templates or residues for the query.
When you have finished adding queries for each chain in the heteromultimer, you can select the queries in the list and build the model. This tab is only available when you select Build a hetero-multimer model.
The Preview Model button quickly builds a model for previewing in the Workspace. No optimization is done and the structure is capped with NMA and ACE at any discontinuities.
The Build Model button runs the job to build the model.
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