computational biochemistry and biophysics - oren m. becker

[...]... 275 ˇ ´ ´ Andras Fiser, Roberto Sanchez, Francisco Melo, and Andrej Sali 15 Bayesian Statistics in Molecular and Structural Biology 313 Roland L Dunbrack, Jr 16 Computer Aided Drug Design 351 Alexander Tropsha and Weifan Zheng Part IV Advanced Applications 17 Protein Folding: Computational Approaches 371 Oren M Becker 18 Simulations of Electron Transfer Proteins 393 Toshiko Ichiye 19 The RISM-SCF/MCSCF... (2) and (3) represents a compromise between simplicity and chemical accuracy Both the bond-stretching and angle-bending terms are treated harmonically, which effectively keeps the bonds and angles near their equilibrium values Bond and angle parameters include b 0 and θ 0, the equilibrium bond length and equilibrium angle, respectively K b and K θ are the force constants associated with the bond and. .. the results obtained from compu- Atomistic Models and Force Fields 9 Figure 1 Hypothetical molecules to illustrate the energetic terms included in Eqs (1)–(3) Molecule A comprises atoms 1–4, and molecule B comprises atom 5 Internal terms that occur in molecule A are the bonds, b, between atoms 1 and 2, 2 and 3, and 3 and 4; angles θ, involving atoms 1–2– 3 and atoms 2–3–4, and a dihedral or torsional... applicability of computational approaches to biomolecules III SCOPE OF THE BOOK The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes The large number of computational tools already available in computational. .. scale, considerable efforts are being made to attain this goal, as overviewed in Chapter 17 Drug design and development is another area of research where computational biochemistry and biophysics are having an ever-increasing impact Computational approaches can be used to aid in the refinement of drug candidates, systematically changing a drug’s structure to improve its pharmacological properties, as well... computational biochemistry and biophysics, has been followed by a large number of theoretical investigations of many complex biomolecular systems It is this large body of work, including the numerous methodological advances in computational studies of biomolecules over the last decade, that largely motivated the production of the present book II OVERVIEW OF COMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICS Although... Design, Biogen, Inc., Cambridge, Massachusetts Alexander D MacKerell, Jr School of Pharmacy, University of Maryland, Baltimore, Maryland Alexey K Mazur Institut de Biologie Physico-Chimique, CNRS, Paris, France xi xii Contributors Francisco Melo Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York Michael Nilges Structural and Computational Biology Program, European Molecular... to the field of computational biochemistry and biophysics for nonspecialists, with the later chapters in Part I presenting more advanced techniques that will be of interest to both the nonspecialist and the more advanced reader Part II presents approaches to extract information from computational studies for the interpretation of experimental data Part III focuses on methods for modeling and designing... 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... given to John A Pople and Walter Kohn for their work in the area of quantum chemistry, signifying the widespread acceptance of computation as a valid tool for investigating chemical phenomena With its extension to bimolecular systems, the range of possible applications of computational chemistry was greatly expanded Though still a relatively young field, computational biochemistry and biophysics is now . 1 Oren M. Becker, Alexander D. MacKerell, Jr., Benoı ˆ t Roux, and Masakatsu Watanabe 2. Atomistic Models and Force Fields 7 Alexander D. MacKerell, Jr. 3. Dynamics Methods 39 Oren M. Becker and. biophysical and biochemical research. Its content repre- sents progress made over the last decade in the area of computational biochemistry and biophysics. Books by Brooks et al. [24] and McCammon and. This work, marking the beginning of modern computational biochemistry and biophysics, has been followed by a large number of theoretical investiga- tions of many complex biomolecular systems. It