Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Volume 3

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Springer Science & Business Media, Nov 30, 1997 - Science - 618 pages
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This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
 

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Contents

Methodology
3
Choice of a method to sample conformational space
10
Assumptions underlying empirical classical interaction functions
25
General constrained dynamics formulation 127
33
General characteristics of the empirical interaction function
34
Forcefield parametrization procedures
62
Conclusions
74
The developmentapplication of a minimalist organicbiochemical
83
Conclusions
299
Simulation versus Xray neutron
305
Dynamics in smallmolecule condensed phases
324
Diffusive motions in molecular crystals
336
Protein dynamics
347
Conclusions
356
Protein structure prediction by global energy optimization
363
Lowenergy alternative fold LEAF hypothesis
369

Comparing the two force fields on complex systems
91
A separating framework for increasing the timestep in molecular
97
Recent LIN progress
105
Summary and Perspective
117
Reduced variable molecular dynamics
122
Traditional constrained dynamics approaches
124
Current modeling approach
129
Conclusions
147
Gaussian shape methods
150
Shape characterization
160
Conclusions
174
Systematic procedure for the development of accurate QMMM
177
Proton transfer in solution
187
Transferability of the QMMM parameters
190
Modeling protonation equilibria in biomolecules
199
Accuracy of the PB method for computing pKas
210
Directions for future investigation
218
Semiexplicit bag model for protein solvation
223
Surface charge approach
226
Boundary integral formulation of dielectric cavity
229
Acknowledgements
242
Application of PoissonBoltzmann solvation forces
244
Example application to a model proteinDNA association
255
Timeaveraging crystallographic refinement
265
Conclusions
268
Incorporation of solvation energy contributions for energy refinement
270
Improvement of the Shrake and Rupley method
276
Normal mode analysis of biomolecular dynamics
284
Harmonic descriptions of biomolecular dynamics
290
Entropy
376
Domain rearrangements
384
Acknowledgements
390
Monte Carlo lattice dynamics and the prediction of protein folds
395
Lattice models of proteins
396
Synergism of the contributions to the potential
403
Folding of ROP monomer
416
Computational tools for structurebased design
433
Obtaining structures
437
Sorting and selecting
443
New trends in computational structure prediction of ligandprotein
451
Conformationally flexible docking of HIV1 protease complexes
457
References
463
Estimation of binding affinity in structurebased design
466
Approaches
469
Insights from calorimetry
489
Computer languages in pharmaceutical design
494
Automatic languagebased approaches Difficulties and limitations
533
How computers can design automatically
539
The objects of prediction and design
544
Available molecular modelling software
550
Conclusions
556
Characterization of the effect of functional groups substitution
563
Computational results
570
Discussion
588
References
598
Author index
603
Subject index
604
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Page xxii - Contact Susan J Buntjer, Conference Coordinator and Supervisor, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037.
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