PACKAGE:charite.christo. PACKAGE:charite.christo.strap. To print this text, click into the text and type CTRL+P or STRG+P. To improve quality of text at the expense of perfromance type CTRL-* (asterisk). The text will appear in the Web-browser and can be printed. To enlarge font type CTRL-+ or rotate the mouse wheel with CTRL+SHIFT. It is recommended to print the overview of context menus BUTTON:StrapAlign#button(CMD_ALL_POPUP)!.

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
For convenience it is recommended to print this help text as explained at the top.
You might want to watch the short movies http://www.bioinformatics.org/strap/#DOCUMENTATION which require the adobe-flashplugin to be installed. Further hints appear in form of WIKI:Tooltips. Information messages which are occasionally shown can be reviewed by typing CTRL+I.

The user interface uses elements of modern desktop applications like MS-Office to make the usage as intuitive as possible. It follows the MS-Windows/Unix conventions. Mac users see bolow.

Macintosh users please note:

Loading proteins

STRAP supports WIKI:Drag_and_drop. Watch movies STRING:ChConstants#MOVIE_Load_Proteins. 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. Watch movies STRING:ChConstants#MOVIE_Load_Proteins_web_uniprot STRING:ChConstants#MOVIE_Load_Proteins_web_pdb. Visit http://www.bioinformatics.org/strap/dragProteinLink.html for details. To close a protein use the context menu (right-click) or mark the protein and hit the DEL-key.

Obtaining protein files

To copy the loaded protein file to the desktop or any other location, the protein label can be dragged to the desktop. Watch movies STRING:ChConstants#MOVIE_Export_Proteins. It is important to drag it first to the left or right side because dragging up and down would 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()

It is recommended to follow the tutorial BUTTON:Tutorials#b("DnD")! at some time.

Aligning sequences

On pressing the tool-button BUTTON:StrapView#button(BUT_ALIGN)! the protein sequences will be aligned using the optimal combination of 3D and sequence methods. The resulting alignment can be exported to the web-browser, text-processor or to Jalview (Ahmed Moustafa PUBMED:14960472) using the tool-button W.

Background information: 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 either the program TM-align (Y Zhang, J Skolnick PUBMED:15849316) or CE (Ilya N. Shindyalov PUBMED:11125099 ported to java by Andreas Prlic). If there is at least one protein file without 3D-information ClustalW (Mark Larkin PUBMED:17576686) or Neobio (Sergio Anibal de Carvalho Junior, http://neobio.sourceforge.net) or Jaligner (Ahmed Moustafa, http://jaligner.sourceforge.net/) is used next respecting the results from TM-align.

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) (WIKIde: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. Watch movie STRING:ChConstants#MOVIE_Drag_protein_to_3D.
When the 3D-view is clicked, its menu-bar appears. This menu-bar contains useful tools like 3D-Superposition.

For proteins given by a sequence file without 3D coordinates 3D-structure cannot be viewed. 3D-structures may be found by WIKI:BLAST against the WIKI:Protein_Data_Bank BUTTON:DialogBlast!. The tool button BUTTON:StrapView#button(BUT_PDB)! opens an assistant to identify a close 3D-structure.

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+left-click or by clicking one protein and typing CTRL-A. Then drag the selected proteins STRING:ChConstants#MOVIE_Drag_to_another_STRAP.

Sequence features like catalytic site residues

Sequence features like active site residues or modified residues can be downloaded from BioDAS* servers or Expasy using the "Sequence features" tool-button. They are displayed as underlinings of the sequences. These underlinings can be dragged with the mouse to another protein or to 3D-structures STRING:ChConstants#MOVIE_Sequence_Features_in_3D. Sequence features have a WIKI:Context_menu STRING:ChConstants#MOVIE_Context_Menu. 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.

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

Full functionality

Clicking the Web-start link in: http://3d-alignment.eu/ to start STRAP as a desktop application. You can exchange proteins between STRAP viewes with the mouse by WIKI:Drag_and_drop. Watch movie STRING:ChConstants#MOVIE_Drag_to_another_STRAP.

Bugs/Problems

Report any problems and suggestions to christophgil@googlemail.com INCLUDE_DOC:charite.christo.Web

Author: christophgil@googlemail.com

  Group for Computational Biochemistry