Proteins computer data banks

A DNA sequence data bank has been established, to supplement the long-established protein sequence data bank, " information from which has been used in several of the above mentioned studies. Heat-capacity data on non-biological molecules has also been entered into a data bank, and from this various thermodynamic functions of the substances may be computed. " Several... 

F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E. Meyer, M.D. Bryce, J.R. Rogers, O. Kennard, T. Shikanouchi and M. Tasumi, The protein data bank A computer-based archival file for macromolecular structures, J. Mol. Biol. 112 (1977), 535-542. 

Bernstein F C, T F Koetzle, G J B Williams, E Meyer, M D Bryce, J R Rogers, O Kennard, T Shikanouchi and M Tasumi 1977. The Protein Data Bank A Computer-Based Archival File for Macromolecular Structures. Journal of Molecular Biology 112 535-542. 

PC Bernstein, TP Koetzle, GIB Williams, EE Meyer, MD Brice, JR Rodgers, O Kennard, T Shimanouchi, M Tasumi. Protein Data Bank Computer based archival file for macromolecular structure. J Mol Biol 112 535-542, 1977. 

Bernstein, F.C., et al. The protein data bank a computer-based archival file for macromolecular structures. 

Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr., Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank A computer-based archival file for macromolecular structures. J Mol Biol 1977 112 535-42. 

R. Moschel, J. J. Stezowski, and D. E. Zacharias for many helpful discussions and collaborations. Most of the diagrams were drawn using the computer programs VIEW (141) and DOCK (142). Figure 21 was drawn with data obtained from the Protein Data Bank, Brookhaven. The work of the author was supported by grants CA-10925, CA-22780, CA-06927, RR-05539 from the National Institutes of Health, BC-242 from the American Cancer Society, and by an appropriation from the Commonwealth of Pennsylvania. 

The Human Genome Project went three-dimensional in late 2000. Structural genomics efforts will determine the structures of thousands of new proteins over the next decade. These initiatives seek to streamline and automate every experimental and computational aspect of the structural determination pipeline, with most of the steps involved covered in previous chapters of this volume. At the end of the pipeline, an atomic model is built and iteratively refined to best fit the observed data. The final atomic model, after careful analysis, is deposited in the Protein Data Bank, or PDB (Berman et ah, 2000). About 25,000 unique protein sequences are currently in the PDB. High-throughput and conventional methods will dramatically increase this number and it is crucial that these new structures be of the highest quality (Chandonia and Brenner, 2006). 

I wish to thank Andrew B. Carrell, who assisted with many of the calculations and figure preparations necessary for the production of this chapter. I also thank H. L. Carrell, G. D. Markham, A. S. Mildvan, and E. K. Patterson for many helpful discussions. Ball-and-stick drawings were drawn with the computer program VIEW (Carrell, 1976). Use of the Cambridge Structural Database (Allen etal., 1979) and the Protein Data Bank (Bernstein el al., 1977) is acknowledged. This work was supported by National Institutes of Health grants GM 44360, CA 10925, and CA 06927 and by an appropriation from the Commonwealth of Pennsylvania. 

Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using on-line protein databases and the three-dimensional molecular viewing utilities Chime and Protein Explorer. If you have not yet installed the Chime plug-in on your computer, go to www.mdlchime.com/chime and follow the instructions for your operating system and browser. Once chime is installed, go to the Protein Data Bank (www.rcsb.org/pdb). 

J. The Protein Data Bank, Three-Dimensional Structures, and Computation ... 

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

Interpretation of results of these studies is still difficult. Results of two-hybrid methods become more useful if they can be coordinated with other approaches. For example, computational methods can predict interactions from genome sequences alone. 11/0 More than 45,000 interactions have been predicted among yeast proteins. Reliable identification of such motifs as DNA-binding domains and Ca2+- binding domains can complement two-hybrid analysis.11 The yeast genome is predicted to contain 162 coiled-coil sequences and at least 213 unique interactions between them.0 Examination of sequences of protein families in the Protein Data Bank (PDB) led to prediction of 8151 interactions of 664 types between protein families in yeast.P... 

For new or would-be users of models, I present in Chapter 11 an introduction to molecular modeling, demonstrating how modern graphics programs allow users to display and manipulate models and to perform powerful structure analysis, even on desktop computers. This chapter also provides information on how to use the World Wide Web to obtain graphics programs and learn how to use them. It also provides an introduction to the Protein Data Bank (PDB), a World Wide Web resource from which you can obtain most of the available macromolecular models. 

Upon request, many authors of published crystallographic structures provide coordinate lists or structure factors by computer mail directly to interested parties. But the great majority of structures are available through the Protein Data Bank (PDB).1 Crystallographers can satisfy publication and funding requirements for availability of their structures by depositing coordinates with this data bank. 

Uhe Protein Data Bank is described fully in F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasume, The Protein Data Bank A computer-based archival file for macromolecular structures, J. Mol. Biol. 112, 535-542, 1977, and E. E. Abola, F. C. Bernstein, S. H. Bryant, T. F. Koetzle, and J. Weng, "Protein Data Bank," in F. H. Allen, F. Bergerhoff, and R. Sievers, eds., Crystallographic Database—Information Content, Software Systems, Scientific Applications, Data Commission of the International Union of Crystallography, Bonn-Cambridge-Chester, 1987, pp. 107-132. 

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