Swiss-PdbViewer

Figure 10.1 Conformation of epothilone D bound in the P450epol< active site. The figure was prepared from PDB entry 1PKF using Swiss-PdbViewer [27]. The heme prosthetic group is shown with its cysteinate ligand (Cys365) bound. For clarity, amino acids lining the active site have been omitted apart from Phe96.

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

Swiss-PdbViewer allows to analyze several proteins at the... 

Plate 1 Stereo photograph of Zif268/DNA complex (see N. P. Pavletich and and C. O. Pabo, Science 252, 809, 1991). (For discussion, see Chapter l. )NOTE Atomic coordinates for preparing this display were obtained from the Protein Data Bank (PDB), which is described in Chapter 7. The PDB file code is lzaa. To expedite your access to all models shown in this book, I provide file codes in this format PDB lzaa. Image created by Swiss-PdbViewer, rendered by POV-Ray. To obtain these programs, see the CMCC Reader s Page. 

Plate 5 Models of the protein thioredoxin (human, reduced form) as obtained from x-ray crystallography (blue, PDB lert) and NMR (red, PDB 3trx). Only backbone alpha carbons are shown. The models were superimposed by least-squares minimization of the distances between corresponding atoms, using Swiss-PdbViewer. (For discussion, see Chapter 3.) Image SPV/POV-Ray. 

DeepView/Swiss-PdbViewer, v. 3.7. http //www.expasy.org./spdv. 

Apart from complete modeling packages (discussed below), only a small number of programs are freely and publicly available from the many methods that have been published (see Table 5.6). Among database methods, this includes only Swiss-PDBViewer [151], and BRAGI which implements the method of Fechteler et al. [128]. Several loop databases are available. Among... 

Swiss-PDBViewer Structure, superposition, alignment and modelling visualization http //www.expasy.ch/spdbv/ SIB, CH, N. Guexetal. [308]... 

Fig. 2. The YPMa trimer shown with trimeric structures of virus capsid proteins and members of the TNF superfamily highlights the diversity of trimerization of jelly roll folds. Only C atoms of the polypeptide chains are shown. Virus trimers were extracted from the Viper database of virus structures (http //viperdb.scripps.edu/) [64], SPMV = Satellite pan-icum mosaic virus STMV = satellite tobacco mosaic virus. Figures 1 and 2 were created using Swiss-PdbViewer [65],... 

Figure 19 Visualization of adaptability of the inner phase of hemicareerand 6 to different guest dimensions through untwisting. From left to right hemieareeplexes 6 benzene, 6 -xylene, and 6 l,4-diiodobenzene. Hemicareerands and cavities were modeled with the program Swiss-PdbViewer. The inner phase and guest volumes as well as the spaee oeeupancy in the inner phase are given for each hemicarceplex.

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