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Deep computing for the life sciences

Vol. 45, No. 3/4, 2001

Order No. G322-0227
Information technology is playing an increasingly important role in the life sciences. This double issue of the of the IBM Journal of Research and Development, and a companion issue of the IBM Systems Journal, illustrate how the use of a computationally intensive, molecular-based approach is advancing research in the life sciences. The issue contains 14 papers that pertain to molecular structure modeling, genomic and proteomic analysis, protein folding, and drug design.
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Table of contents  
Papers may be viewed by clicking on the title of interest
Preface William C. Swope, James M. Coffin, and Barry Robson, Guest Editors p. 363
Model studies of the structures, reactivities, and reaction mechanisms of metalloenzymes K. Morokuma, D. G. Musaev, T. Vreven, H. Basch, M. Torrent, and D. V. Khoroshun p. 367
DFT-based molecular dynamics as a new tool for computational biology: First applications and perspective W. Andreoni, A. Curioni, and T. Mordasini p. 397
Quantum crystallography, a developing area of computational chemistry extending to macromolecules L. Huang, L. Massa, and J. Karle p. 409
Interfacing molecular dynamics with continuum dynamics in computer simulation: Toward an application to biological membranes G. S. D. Ayton, S. Bardenhagen, P. McMurtry, D. Sulsky, and G. A. Voth p. 417
The adaptive multilevel finite element solution of the Poisson–Boltzmann equation on massively parallel computers N. A. Baker, D. Sept, M. J. Holst, and J. A. McCammon p. 427
Brute force estimation of the number of human genes using EST clustering as a measure D. B. Davison and J. F. Burke p. 439
Hidden Markov models in biological sequence analysis E. Birney p. 449
DELPHI: A pattern-based method for detecting sequence similarity A. Floratos, I. Rigoutsos, L. Parida, and Y. Gao p. 455
Evaluating protein structure-prediction schemes using energy landscape theory M. P. Eastwood, C. Hardin, Z. Luthey-Schulten, and P. G. Wolynes p. 475
Protein flexibility and electrostatic interactions S. Kumar, H. J. Wolfson, and R. Nussinov p. 499
A hierarchical, building-block-based computational scheme for protein structure prediction C.-J. Tsai, B. Ma, Y. Y. Sham, S. Kumar, H. J. Wolfson, and R. Nussinov p. 513
Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins B. Fain, Y. Xia, and M. Levitt p. 525
QSAR in grossly underdetermined systems: Opportunities and issues D. E. Platt, L. Parida, Y. Gao, A. Floratos, and I. Rigoutsos p. 533
Multiobjective optimization of combinatorial libraries D. K. Agrafiotis p. 545
Recent publications by IBM authors p. 567
Patents p. 575