Economou Lab-Teaching BIO501


BIO501

 

SwissPDB Viewer-an introduction

Basic skills for the retrieval of protein 3D structure files (pdb) and analysis of protein structures

Molecular Biology and Biomedicine and Protein Biotechnology  

 

Swiss-PdbViewer (or DeepView) is a molecular structure viewer with a user-friendly interface.

Macromolecules can be: visualized in several formats, coloured , rotated, mutated, truncated, superimposed with homologues etc. It is available for Mac, PC and Linux (download).

Useful SwissPDB Viewer sites:

Home
Basic Tutorial (strongly recommended)

Advanced Tutorial

Discussion List

Tips

Downloading pdb files:

Protein structures are determined either by X-ray crystallography or by NMR. The data describing the three dimensional co-ordinates for all the atoms of the protein is contained in a pdb (protein data bank) file that has a name like "1XMN.pdb". To download protein structure files that can be viewed and modified with SwissPDB Viewer on your computer:

If you only have the name of the protein>

PubMed (chose "Structure" from the drop down menu left of the query window and write protein name in the query window) or

PubMed-Structure

If you know the file name of the structures>

RCSB-PDB (write the file name in the query window)

PDBsum (write the file name in the query window)

For more protein structure-related links

For more protein-related links