Computational biochemistry

Biochemistry-Data processing. 2. Biochemistry-Computer simulation. 3. Biochemistry-Mathematics. I. Title. 

Free energy perturbation (FEP) theory is now widely used as a tool in computational chemistry and biochemistry [91]. It has been applied to detennine differences in the free energies of solvation of two solutes, free energy differences in confonnational or tautomeric fonns of the same solute by mutating one molecule or fonn into the other. Figure A2.3.20 illustrates this for the mutation of CFt OFl CFt CFt [92]. 

Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 02-106 Warsaw, Poland Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365, USA... 

M. H. Hao, M. R. Pincus, S. Rackovsky, and H. A. Scheraga. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry, 32 9614-9631, 1993. 

The classical introduction to molecular mechanics calculations. The authors describe common components of force fields, parameterization methods, and molecular mechanics computational methods. Discusses th e application of molecular mechanics to molecules comm on in organic,and biochemistry. Several chapters deal w ith thermodynamic and chemical reaction calculations. 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

In combination, the book should serve as a useful reference for both theoreticians and experimentalists in all areas of biophysical and biochemical research. Its content represents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and Harvey [25] are recommended for an overview of earlier developments in the field. Although efforts have been made to include the most recent advances in the field along with the underlying fundamental concepts, it is to be expected that further advances will be made even as this book is being published. To help the reader keep abreast of these advances, we present a list of useful WWW sites in the Appendix. 

Naturally, the pivotal role of protein folding in biophysics and biochemistry has yielded a very large body of research. In this chapter we focus primarily on the different theoretical and computational approaches that have contributed to the current understand-... 

It is well known that the resources available on the Internet are in constant flux, with new sites appearing on a daily basis and established sites disappearing almost as frequently. This also holds true for the dedicated tools used in biochemical and biophysical studies. New tools are constantly becoming available, and established tools, obsolete. Such rapid change makes it difficult to stay current with the state-of-the-art technologies in the areas of bioinformatics and computational biochemistry and biophysics. 

The first dynamical simulation of a protein based on a detailed atomic model was reported in 1977. Since then, the uses of various theoretical and computational approaches have contributed tremendously to our understanding of complex biomolecular systems such as proteins, nucleic acids, and bilayer membranes. By providing detailed information on biomolecular systems that is often experimentally inaccessible, computational approaches based on detailed atomic models can help in the current efforts to understand the relationship of the strucmre of biomolecules to their function. For that reason, they are now considered to be an integrated and essential component of research in modern biology, biochemistry, and biophysics. 

Ghose, T.K., Bioprocess Computation in Biotechnology , vol. 1. Ellis Horwood Series in Biochemistry and Biotechnology, New York, 1990. 

The book can be used in a one semester course for senior undergraduate and graduate students who are interested in understanding physical aspects of biochemistry and computer modeling of macromolecules. It can also be... 

The latter part of the 20th century has seen remarkable advances in science and technology. Accomplishments in biochemistry and medicine, computer technology, and telecommunications have benefited nearly everyone on Earth to one degree or another. Along with these advances that have improved our quality of life, scientific research into the study of the Earth has revealed a planetary system that is more complex and dynamic than anyone would have imagined even 50 years ago. The Earth and the environment have become one of society s greatest concerns, perhaps as the result of these discoveries combined with the quick dissemination of information that is now possible with modem telecommunications. 

Boyd DB. Beta-lactam antibacterial agents Computational chemistry investigations. In Greenberg A, Breneman CM, Liebman JF, editors. The amide linkage Structural significance in chemistry, biochemistry, and materials science. New York Wiley, 2000. p. 337-75. 

Medvedev AE, Veselovsky AV, Shvedov VI, Tikhonova OV, Moskvitina TA, Fedotova OA, et al. Inhibition of monoamine oxidase by pirlindole analogues 3D-QSAR and CoMFA analysis. / Chem Inf Comput Sci 1998 38 1137-44. Miller JR, Edmondson DE. Structure-activity relationships in the oxidation of para-substituted benzylamine analogues by recombinant human liver monoamine oxidase A. Biochemistry 1999 38 13670-83. 

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