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Introduction

With this viewer you can
  1. View and align amino acid sequences,
  2. Display, superimpose and align 3D-structures of proteins from the PDB-database,
  3. Export sequence alignments to the text-processor or to Jalview (Michele Clamp: PUBMED:14960472)
  4. Identify remote homologs
You might want to watch the Shockwave Flash demo animations at http://www.bioinformatics.org/strap/swf/. For convenience it is recommended to print this help text as explained at the top. Further help is provided by WIKI:Tooltips. Information messages which are occasionally shown can be reviewed by typing CTRL+I.

The user interface follows the paradigms of office applications to make the usage as intuitive as possible. It implements

For Macintosh mice that have only one button context menus are opened with CTRL+ALT+left-click.

Loading proteins

STRAP supports WIKI:Drag_and_drop: Drag a file with the mouse from a file browser or from the desktop to the STRAP application frame. Release the mouse over the alignment panel. The dropped protein will be loaded and the amino acid sequence appears in the alignment-panel. A unique feature is that protein links from Bioinformatics resources can be dragged directly into STRAP. Visit http://www.bioinformatics.org/strap/dragProteinLink.html for details. To close a protein use the context menu (right-click).

Copying protein files

To copy the loaded protein file to the desktop or any other location you can drag the protein label sidewards to the desktop. It is important to drag it first to the left or right since dragging up and down only changes the order of alignment-rows. Also see the downloaded protein files in the working directory of the current STRAP session: STRING:ChUtils#dirWeb()

Aligning sequences

On pressing the tool-button BUTTON:StrapView#button(BUT_ALIGN)! the protein sequences will be aligned. If a few proteins are selected in STRAP, only the selected proteins are aligned. If there are at least two protein files with 3D-coordinates the alignment is performed by superimposing the 3D-structures upon each other using the program TM-align (Y Zhang, J Skolnick: PUBMED:15849316). If there is at least one protein file without 3D-information ClustalW (PUBMED:17576686) is used next respecting the results from TM-align. The resulting alignment can be exported to the web-browser, text-processor or to Jalview (PUBMED:14960472) using the tool-button BUTTON:"<i><b><font color=0000FF>W</font></b></i>".

Protein names and icons

Open dialog "file => Rename" in the context menu of protein labels (right-click). The rename dialog provides several additional rename options like displaying the organism name in the protein name. INCLUDE_DOC:ChIcon

Copying amino acid sequence

To get the entire sequence in WIKI:Fasta-format the alignment cursor must be on the respective sequence and CTRL+C (C for "copy") need to be typed typed. To copy a sequence segment to the WIKI:Clipboard_(software) (Zwischenablage) select the amino acids with the mouse. From the clipboard it can be pasted into other applications with CTRL+V.

Displaying 3D-structures

For protein files with 3D-coordinates (PDB-format) 3D-views can be opened by pressing BUTTON:StrapView#button(BUT_WIRE)!. To get a further protein into the same 3D view drag the protein file or the protein label into the 3D-view. To compare the proteins three-dimensionally press the button "superimpose".

For proteins given by a sequence file without 3D coordinates 3D-structure cannot be viewed. For some sequence files appropriate 3D-structures may be found by WIKI:BLAST against the WIKI:Protein_Data_Bank BUTTON:DialogBlast!.

Identifying catalytic site residues in 3D structures

The catalytic site residues are highlighted red. The balloon text and double click show detailed information. The positions are obtained from the catalytic site atlas (C.T. Porter, G.J. Bartlett and J.M. Thornton, PUBMED:14681376). Those with evidences in the literature are marked bright red.

Database links

A few database links are generated from the PDB-ID and the EC-number and appear by click on the left edge of the protein name.

Hetero compounds and DNA/RNA

Many PDB entries contain ligands like FMN, FAD and Metal ions or DNA/RNA. These proteins are marked by a green (for DNA/RNA) or red mark at the left.

Saving the alignment project:

In Web mode the alignment data is lost after the STRAP session. However, you can run a full STRAP-session by clicking the Web-start link in: http://3d-alignment.eu/. You will be asked for a project directory where the data is stored. The complete alignment can be transfered by WIKI:Drag_and_drop. For this purpose select all proteins. This is done by clicking the first one with left click and the last protein with shift-key left click. Then drag the selected proteins.

Full functionality

Users can enable full STRAP functionality using the "Options" tool-button. In full STRAP mode the menu-bar and additional control elements become visible.

Bugs/Problems

Report any problems and suggestions to christoph.gille@charite.de INCLUDE_DOC:charite.christo.Web

Author: Christoph.Gille@charite.de

  Group for Computational Biochemistry