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

W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson

Springer, Nov 30, 1997 - Technology & Engineering - 644 pages

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.

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
• 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
• 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
• 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

Popular passages

Page xxii - Contact Susan J Buntjer, Conference Coordinator and Supervisor, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037.‎

Page xix - Genentech, Inc., 460 Point San Bruno Boulevard, South San Francisco, CA 94080.‎

Bibliographic information

• Title: Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Volume 3; Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Paul K. Weiner; Volume 3 of Computer Simulations of Biomolecular Systems, Wilfred F. van Gunsteren
• Editors: W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson
• Contributors: W.F. van Gunsteren, P.K. Weiner, Tony Wilkinson
• Edition: illustrated
• Publisher: Springer, 1997
• ISBN: 9072199251, 9789072199256
• Length: 644 pages
• Subjects: Science / Chemistry / General; Science / Chemistry / Physical & Theoretical; Science / Life Sciences / Biochemistry; Science / Life Sciences / Zoology / General; Technology & Engineering / Textiles & Polymers