When a protein amino acid sequence is pasted into the textarea, the input text is immediately validated and if valid replaced with an interactive sequence view.
The format of the sequence must be either FASTA, Clustal or raw sequence.
You may also upload the sequence as a file.
As an example, we will paste the sequence:
>Target SNAGNSTTSDKGTEEATTSAFDVMSQFNEIGVSYPLTVTDQAGRTVTFEKAPEKIASSYYISTSLLLALGLQ DKLVGIEAKANTRNIYKLAAPAIVSLPNMGTAKEFNTEACVAATPDVVFLPMKLKKTADTLESLGIKAVVVN PEDQSLLEECITLVGKITNNAGRAEALNNSIKTFLADNKTNVSGGNTPSVYLAGNSSVLSTAGSKMYQNTLL TNAGGKNVASELTDTYWANVSYEQILAWNPDYIVIAADATYTVDDILNDANLAGCNAVKNKNVVKLPNNIEA WDSPVPGSFLGSIYIASVLHPEKVTKDFYETCVTKFYESFYGFTPAK
If the desired template for modelling is known and is found in the SMTL, an alignment of target-template in either FASTA or Clustal format may be used to start modelling without the need for a template search.
1: Preferably the first sequence in alignment should be the target protein amino acid sequence.
2: Preferably the template sequence(s) are named as per PDB id format. eg "1CRN", "1CRNA" or "1CRN_A".
3: If a valid target-template alignment is identified by SWISS-MODEL, the alignment will be displayed. Otherwise, please specify the target and/or template from a drop down list which will be displayed.
4: It is possible there are more than one biounits for your template, if so you will see several alignments from which you must make a selection to build a model.
As an example we will paste the following target/template alignment:
>THN_DENCL KSCCPTTAARNQYNICRLPGTPRPVCAALSGCKIISGTGCPPGYRH >1crnA TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
When a UniProtKB AC is pasted in the textarea, the input is immediately validated and replaced with an interactive sequence view.
As an example, we will paste the UniProtKB AC P61851
It is possible to specify the structure to be used as modelling template by uploading a file in PDB format (*) with coordinates of the template structure.
1: Enter the target protein amino acid sequence as normal in the textarea.
>sp|P61851|SODC_DROME MVVKAVCVINGDAKGTVFFEQESSGTPVKVSGEVCGLAKGLHGFHVHEFGDNTNGCMSSG PHFNPYGKEHGAPVDENRHLGDLGNIEATGDCPTKVNITDSKITLFGADSIIGRTVVVHA DADDLGQGGHELSKSTGNAGARIGCGVIGIAKV
2: Upload your template file.
Oligomeric templates are accepted, it is possible to build heteromers by adding multiple target sequences to the input.
If the file is not accepted, you may first try removing non-standard residues (HETATMS).
The program DeepView (Swiss-PdbViewer, Guex et al.) can be used to generate, display, analyze and manipulate modelling 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 therefor 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.
Here is an example DeepView Project file.
DeepView can be downloaded from the DeepView Home website.
It is possible to input multiple sequences to model an hetero-oligomer or a protein complex.
1: Enter the first target protein amino acid sequence or UniProt AC as normal in the textarea.
2: Hit the "Add Hetero Target" button and enter an additional amino acid sequence.
>HBB_PHYMC P09905 Hemoglobin subunit beta-1/2 VHLTGEEKSGLTALWAKVNVEEIGGEALGRLLVVYPWTQRFFEHFGDLSTADAVMKNPKVKKHGQKVLASFG EGLKHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVVVLARHFGKEFTPELQTAYQKVVAGVANALAHK YH
3: Repeat Step 2 untill you entered the amino acid sequences of all the interacting partners.