SWISS-MODEL

Display of template identification results

A condensed graphical view of the modeling task is provided containing the target sequence, the template matches sorted and colored according to the associated E-value, and the InterPro mappings. Clickable bars indicate the matched regions and guide the user to the underlying original program output.

In the InterPro output a link leads to the detailed InterPro page for this entry.

In the output of the different template identification programs the template annotations (via the link to the SWISS-MODEL Template library) and target-template alignment can be retrieved.

Alignments can be obtained as DeepView project file. The latter allows the user to visualize the different alignments in the structural context of the template, to correct misplaced insertions and deletions, and to manually adjust misaligned regions. The modified project can then be saved to disk and submitted as "project mode" to the workspace for model building by the SWISS-MODEL pipeline.

When searching a clustered version of the SWISS-MODEL Template library (e.g. ExPDB90) only the alignment between the target sequence and the sequence of the representative of the cluster is shown. Information about the members of the cluster is presented in the detailed output of the different template search programs. For each template, the SWISS-MODEL workspace provides a summary showing a small ribbon representation, experimental details, information about bound molecules, as well as links to PDB (Westbrook et al.), SCOP (Andreeva et al.), CATH (Pearl et al.), PDBsum (Laskowskiet et al.), and MSD (Velankaret et al.).

Model building

Depending on the difficulty of the modelling task, three different types of modelling requests (automated mode, alignment mode, project mode) are provided, which differ in the amount of user intervention.

Modelling requests are computed by the SWISS-MODEL server homology modelling pipeline (Schwede et al.).

Automated Mode

The "automated mode" is suited for cases where the target-template similarity is sufficiently high to allow for fully automated modelling. As a rule of thumb, automated sequence alignments are sufficiently reliable when target and template share more than 50% percent of sequence identity.

This submission requires only the amino acid sequence or the UniProt accession code of the target protein as input data. The pipeline will automatically select suitable templates based on a Blast (Altschul et al.) E-value limit (which can be adjusted upon submission), experimental quality, bound substrate molecules, or different conformational states of the template.

Depending on the planned model application, it can be necessary to select a different structural template than the one ranked first in the automated process. Typical examples are proteins in different conformational states, e.g. 1ake vs. 4ake. It is possible to specify the structure to be used as modelling template either by identifying an entry in the SWISS MODEL Template library by PDB-ID + ChainID e.g. "1ake" chain "A", or by uploading a file in PDB format (*) with coordinates of the template structure. Please make sure that this file contains only a single protein chain, and does not contain chemically modified amino acids, hereto atoms, ligands, etc.

(*) A simple PDB-like file containing the coordinates of the template structure. For more information about PDB file format please see link: http://www.wwpdb.org/docs.html

Alignment Mode

Multiple sequence alignments are a common tool in many molecular biology projects. If the three-dimensional structure is known for at least one of the members, this alignment can be used as starting point for comparative modelling using the "alignment mode".
The "alignment mode" allows the user to test several alternative alignments and evaluate the quality of the resulting models in order to achieve an optimal result.

In order to facilitate the use of alignments in different formats, the submission is implemented as a three step procedure:

1. Prepare a multiple sequence alignment.

• It must contain at least your target sequence and the template sequence
• Use any of your favorite alignment tools. We recommend T_COFFEE by Cedric Notredame
• Make sure the sequence names are "reasonable"

2. Submit your alignment to the Workspace Alignment Mode.

• Possible formats are: FASTA, MSF, CLUSTALW, PFAM and SELEX
• You may either upload your file or cut & paste
• Don't forget to specify the correct alignment format
• Here is a small example for testing (cut & paste):

CLUSTAL W (1.82) multiple sequence alignment

THN_DENCL       KSCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH- 46
THNX_TEST       KSCCPDTTGRDIYNTCRFGGGSRQVCARISGCKIISASTCPS-YPNK 46
1crnA           TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN- 46
                .:***  ..*  :  **: * .. :**  :** **..: **  *   

3. Select Target and Template

• The alignment (as it was interpreted by the server) should now be displayed in the bottom part of the page.
• The script will try to make a good guess for the correct names based on your submission.
• Select the sequence name of the target sequence (e.g. THN_DENCL)
• Select the sequence of the template structure (e.g. 1crnA). You don't need to use PDB IDs, you may use any name you like.
• Specify the template structure to which this sequence belongs. This template MUST be part of the ExPDB template library. Please use the SWISS-MODEL Template library tool to check...
• Don't forget to specify the correct CHAIN ID. Note that PDB's chain IDs are normally in capital letters.

Target  sequence:       
Template sequence:PDB-Code:Chain-ID: 

4. Check Alignment and Submit

• The alignment at the bottom of the page should represent the correct mapping of the template structure on the target sequence. Please check carefully before submission.
• As usual, please provide name and e-mail for the SWISS-MODEL submission.
• Good Luck with your model ....

The following formats are currently supported: FASTA, MSF, CLUSTALW, PFAM and SELEX;

Examples:

fasta:

>THN_DENCL
KSCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH-
>THNX_TEST
KSCCPDTTGRDIYNTCRFGGGSRQVCARISGCKIISASTCPS-YPNK
>1crnA
TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN-

clustal:

CLUSTAL W (1.82) multiple sequence alignment

THN_DENCL       KSCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH- 46
THNX_TEST       KSCCPDTTGRDIYNTCRFGGGSRQVCARISGCKIISASTCPS-YPNK 46
1crnA           TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN- 46
                .:***  ..*  :  **: * .. :**  :** **..: **  *   

 !!AA_MULTIPLE_ALIGNMENT 1.0

  thn_dencl.msf MSF:  47 Type: P 08/08/05 CompCheck:  427 ..

  Name: THN_DENCL  Len: 47  Check: 8212 Weight: 1.00
  Name: THNX_TEST  Len: 47  Check: 5295 Weight: 1.00
  Name: 1crnA      Len: 47  Check: 6920 Weight: 1.00

//

           1                                            47
THN_DENCL  KSCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH~
THNX_TEST  KSCCPDTTGRDIYNTCRFGGGSRQVCARISGCKIISASTCPS.YPNK
1crnA      TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN~

Project Mode

In difficult modeling situations, where the correct alignment between target and template cannot be clearly determined by sequence based methods, visual inspection and manual manipulation of the alignment can significantly help improving the quality of the resulting model.

Project files contain the superposed template structures, and the alignment between the target and template. Project files can be generated inside the program DeepView (Swiss-PdbViewer Guex et al.), by the workspace template selection tools, and are also the default output format of the modeling pipeline. This allows analyzing and iteratively improving the the models generated by the "Automated mode" and "Alignment mode" modeling approaches.

The program DeepView can be downloaded freely from the tools section or from the ExPASy web site .

DeepView

The program DeepView (Swiss-PdbViewer, Guex et al.) can be used to generate, display, analyze and manipulate modeling project files for the SWISS-MODEL workspace.

Project files contain the superposed template structures, and the alignment between the target and template. The user has therfor full control over essential modelling parameters, i.e. the choice of template structures, the correct alignment of residues, and the placement of insertions and deletions in the context of the three-dimensional structure.

Project files can be generated inside DeepView, by the workspace template identification tools, and are also the default output format of the modeling pipeline. This allows analyzing and iteratively improving the output of the different modeling tools.

DeepView allows to visualize the model and the templates, and to analyse certain structural features e.g. Ramachandran plots or electrostatic properties. Moreover, it allows adjusting manually the placement of insertions and deletions in the alignment on which the initial modelling process was based on. The project with the modified alignment can then be re-submitted to the SWISS-MODEL workspace for model building.

DeepView can be downloaded at: http://www.expasy.org/spdbv/

DeepView does not require administrator privileges for installation. E.g. under MS windows, simply uncompress the distributed archive at any location you like (e.g. c:\spdbv or on your desktop) and start working by starting the spdbv.exe application.

MVEIVYWSGTGNTEAMANEIEAAVKAAGADVESVRFEDTNVDDVASKDVILLGCPAMGSE
ELEDSVVEPFFTDLAPKLKGKKVGLFGSYGWGSGEWMDAWKQRTEDTGATVIGTAIVNEM
PDNAPECKELGEAAAKA

- FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol:

>sp|P00321|FLAV_MEGEL Flavodoxin - Megasphaera elsdenii.
MVEIVYWSGTGNTEAMANEIEAAVKAAGADVESVRFEDTNVDDVASKDVILLGCPAMGSE
ELEDSVVEPFFTDLAPKLKGKKVGLFGSYGWGSGEWMDAWKQRTEDTGATVIGTAIVNEM
PDNAPECKELGEAAAKA

- UniProt Accesion number: P00321

Display of modeling results

Coordinates of the model, the underlying alignment, log files, and quality evaluations can be accessed and downloaded via web-browser from the workspace.

Model Details

This section gives access to display the model and download its coordinates.

The model coordinates are available in two different formats:

• DeepView project files (recommended).
• PDB format

PDB formatted protein models can be displayed by any molecular visualization tool or browser-plugin. Here is a short list of freely available software:

• DeepView (MS Windows, Macintosh, Linux)
• DINO (Linux, IRIX, OSF,SUN)
• Rasmol (MS Windows, Mac, Unix)
• CHIME Plugin (requires registration)

If the model has been build using the Automated Mode, information about the template(s) used for modeling is provided with cross references to structural information databases via the link to the SWISS MODEL Template library.

Alignment Output

Displays the target template sequence alignment used in the modeling procedure and the assigned secondary structure.

Modeling Log

The modeling log gives a detailed description of the individual modeling steps. The models are built using the SWISS-MODEL server pipeline (Schwede et al.). The modelling log shows the individual steps during model building Guex et al., especially which parts of the model have been built ab initio (i.e. insertions / deletions).

Template SelectionLog

The logfile provides information about the template selection step to search the SWISS-MODEL Template library for suitable templates.

Protein Structure & Model Assessment Tools

Evaluation of model quality is a crucial step in homology modeling. While the performance of the automated SWISS-MODEL (Schwede et al.) pipeline in general is continuously evaluated by the EVA project (Koh et al.), the quality of individual models can vary significantly.

Therefore, graphical plots of Anolea mean force potential (Melo et al.) and GROMOS empirical force field energy (van Gunsteren et al.) are provided to enable the user to estimate the local quality of the predicted structure. The stereochemistry of protein models and template structures can be analysed with Whatcheck (Hooft et al.) and Procheck ( Laskowski et al.). In order to be able to rank alternative models of the same target, pseudo energies for the entire model as calculated by QMEAN (Benkert et al.) and DFIRE (Zhou et al.) are provided as well. To facilitate the description of template and model structures, DSSP (Kabsch et al.) and Promotif (Hutchinson et al.) can be invoked to classify structural features.

Anolea

The atomic empirical mean force potential ANOLEA (Melo et al.) is used to assess packing quality of the models. The program performs energy calculations on a protein chain, evaluating the "Non- Local Environment" (NLE) of each heavy atom in the molecule.

The y-axis of the plot represents the energy for each amino acid of the protein chain. Negative energy values (in green) represent favourable energy environment whereas positive values (in red) unfavourable energy environment for a given amino acid.


QMEAN

QMEAN (Benkert et al.) is a composite scoring function for the estimation of the global model quality. QMEAN consisting of five structural descriptors: The local geometry is analysed by a torsion angle potential over three consecutive amino acids. A distance-dependent pairwise residue-level potential is used to assess long-range interactions. A solvation potential describes the burial status of the residues. Two simple terms describing the agreement of predicted and calculated secondary structure and solvent accessibility, respectively, are also included.

QMEAN returns a pseudo energy of the whole model which can be used in order to compare and rank alternative models of the same target. The lower the predicted energy, the better model. Additionally, the pseudo energies of the five contributing terms are provided.

DFire

DFIRE (Zhou et al.) is an all-atom statistical potential based on a distance-scaled finite ideal-gas reference state. DFIRE is used to assess non-bonded atomic interactions in the protein model.

A pseudo energy for the entire model is provided which reflects the quality of the model and can be used for ranking alternative predictions of the same target. A lower energy indicates that a model is closer to the native conformation.

Gromos

GROMOS (van Gunsteren et al.) is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems and can be applied to the analysis of conformations obtained by experiment or by computer simulation.

The y-axis of the plot represents the energy for each amino acid of the protein chain. Negative energy values (in green) represent favourable energy environment whereas positive values (in red) unfavourable energy environment for a given amino acid.