Swiss PDB Viewer

Swiss-Pdb Viewer An application that provides a user-friendly interface... 

Guex, N., Diemand, A., Peitsch, M. C., and Schwede, T. Deep View Swiss Pdb Viewer. Basel Swiss Institute of Bioinformatics, 2001. Available on line at www.expasy.org/ spdbv/. 

Swiss-PDB viewer This program is available at http //www.expasy.org/spdbv/. 

Fig. 1. Crystal structure of the biotin carboxyl carrier protein domain of Escherichia coli. The N- and C-termini and, 50A away, the single lysine residue that is biotinylated in vivo can all clearly be seen. Figure prepared from PDB file 1BDO using Swiss PDB Viewer (19).

Figure 14.12. Superimposition of molecular structures with HyperChem. Pigeon lysozyme structure (red) derived from homology modeling with Swiss-PDB Viewer is overlapped against chicken lysozyme structure, pdb1 lyz.ent (black). Two catalytic residues, Glu35 and Asp 52 (chicken lysozyme), are highlighted (green).

This chapter focuses on the application of molecular modeling to calculate, manipulate, and predict protein structures and functions. Concepts of structure similarity/ overlap, homology modeling, and molecular docking, which are special concerns of protein biochemists, are considered. Approaches to protein modeling by the use of two programs (Swiss-Pdb Viewer and KineMage) and two online servers (B and CE) are described. 

Figure 15.1. Workspace of Swiss-PDB Viewer. The workspace of Swiss-PDB Viewer (SPBBV) consists of main windows (with menu bars, icons, and display window), control panel (with listing of amino acid residues), and align window (with amino acid sequence of the displayed molecule). Lysozyme (1 lyz.pdb) with highlighted catalytic residues (Glu35 and Asp52) is displayed.

Swiss-Pdb Viewer http //expasy.ch/spdbv/text/getpc.htm... 

Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-Pdb viewer an environment for comparative protein modeling. Electrophoresis 18 2714-2723... 

Kaplan W, Littlejohn TG. Swiss-PDB Viewer (Deep View). Brief Bioinform 2001 2 195-7. 

Fig. 12.3 Overlay of X-ray structures of hCypl 8 complexed with Suc-Ala-Ala-Pro-Phe-pNA (red), CsA (blue), Gag CA[81—105] fragment (green), and SFA (cyan) using the Swiss PDB Viewer Software 3.7b2, Glaxo-Wellcome). Only essential residues which contract H-bonds with the ligand are shown.

Figure 14-1. Atomic structure and reduced representation in terms of a graph of peaks of a protein chain (PDB file 1B69). The peaks are coloiu-coded per amino-acid type. Visualizations of the atomic and reduced representations were obtained on combining the Swiss PDB Viewer (http //www.expasy.org/ spdbv) and the ray-tracing POV-Ray (http //www.povray.org) programs (see color plate section)...

PDB Viewer An Environment for Comparative Protein Modeling. Download the Swiss-PDB Viewer from http //swissmodel.expasy.org/spdbv/mainpage.htm. 

In the Chapter 19 Lagniappe, we discussed how to access enzyme structural data from the Protein Data Bank. Once the data for a specific enzyme have been located, it s then possible to visualize, manipulate, and study the structure. You can do this either by downloading the data file to your own computer and opening it with a free visualization program, such as DeepView (Swiss PDB Viewer)... 

---