Introduction

Mixed sequence/3D-structure alignments can be computed conveniently by pressing the tool-button JCOMPONENT:StrapView#button(BUT_ALIGN)!. Please apply the tool-button to the example files BUTTON:Tutorials#bExampleFiles("13")!.

By pressing this button two computational steps are performed automatically. In this tutorial the two steps are performed manually.

Aligning the PDB-files three-dimensionally

The 3D-coordinates are used to make a multiple sequence alignment with the superposition program CE or TM-align. Though the sequences are very different, the WIKI:Protein_structures are similar enough to perform a WIKI:Structural_alignment. Chose the alignment method COMBO:Superimpose_native_CE or COMBO:Superimpose_CEPROXY in the dialog BUTTON:DialogAlign! In this dialog select all proteins with the file suffices ".dssp" or ".pdb" or ".ent". Invoke computation with the button LABEL:ChButton#BUTTON_GO. After successful computation a preview with the resulting alignment is shown. Press the button LABEL:DialogAlignResult#BUT_LAB_Apply.

Aligning all proteins

Currently, only the proteins with a 3D-structure are aligned. This alignment will be used as a profile in the following step.

Creating the profile: Go to BUTTON:DialogExportAlignment! and generate the alignment of the proteins with 3D-structure in ClustalW format. To avoid that long lines are folded choose a large number for "Residues per line". Copy the alignment into the text-area for profiles and remove the protein names. Keep only the gapped sequences.

Aligning with the Profile: Return to the main tab of the dialog BUTTON:DialogAlign!. Chose the alignment method: WIKI:ClustalW or COMBO:MultipleAlignerT_Coffee and Select all proteins in the alignment dialog. Activate the first check-box CB:"profile 1". When the check-boxes are activated a text-area appears where the profile can be typed in. Now you can start the computation LABEL:ChButton#BUTTON_GO. The resulting alignment includes all proteins and respects the previous result of the 3D-alignment.