Protein Data Bank 178 INDEX

Figure 2.29. Detail of photosystem I, seen from the side, with the division between units A and B (see Fig. 2.27) in the middle. Chlorophyll molecules (chi) other than the six central ones involved in transfer of energy to the three Fe4S4 clusters (FeS) are omitted. Chlorophylls, phylloquinones (phy, also known as vitamin K) and iron-sulphur clusters are further indexed with the subimit label A, B or X (cf. Fig. 2.27), and the chlorophylls are shown with an index number 1 to 3. Other identified molecules include LHG (CggHygOjoP), LMG (C45H84OJQ) and a number of p-carotenes (BCR). The scattered dots are oxygen atoms of water molecules (no hydrogens are shown). Based on Protein Data Bank ID IJBO Jordan et ah, 2001).

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

RCSB, Protein Data Bank, operated by the Research Collaboratory for Structural Bioinformatics, http //www.rcsb.org/pdb/index.html. 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

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