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Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding
Edited by: P. M. Pardalos, D. Shalloway, and G. Xue
A co-publication of the AMS and DIMACS.

DIMACS: Series in Discrete Mathematics and Theoretical Computer Science
1996; 271 pp; hardcover
Volume: 23
ISBN-10: 0-8218-0471-5
ISBN-13: 978-0-8218-0471-1
List Price: US$83
Member Price: US$66.40
Order Code: DIMACS/23
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This book contains refereed papers presented at a remarkable interdisciplinary scientific meeting attended by a mix of leading biochemists and computer scientists held at DIMACS in March 1995. It describes the development of a variety of new methods which are being developed for attacking the important problem of molecular structure.


  • Focuses on global optimization algorithms and heuristics for molecular conformation and protein folding problems
  • Presents the most efficient recent algorithms
  • Covers a spectrum of algorithmic issues and applications

Co-published with the Center for Discrete Mathematics and Theoretical Computer Science beginning with Volume 8. Volumes 1-7 were co-published with the Association for Computer Machinery (ACM).


Graduate students and researchers in mathematics, molecular biology, biochemistry, computer science, engineering, and operations.


"Reflects ... much of the state-of-the-art ... highly recommended to graduate students and researchers in mathematical programming, molecular biology, biochemistry, computer science, engineering and operations research."

-- Journal of Global Optimization

Table of Contents

  • P. Amara, J. Ma, and J. E. Straub -- Global minimization on rugged energy landscapes
  • R. E. Bruccoleri -- Energy directed conformational search of protein loops and segments
  • R. H. Byrd, E. Eskow, A. van der Hoek, R. B. Schnabel, C.-S. Shao, and Z. Zou -- Global optimization methods for protein folding problems
  • B. W. Church, M. Orešič, and D. Shalloway -- Tracking metastable states to free-energy global minima
  • J. Gu and B. Du -- A multispace search algorithm for molecular energy minimization
  • H. A. Hauptman -- A minimal principle in the phase problem of X-ray crystallography
  • X. Hu, D. Xu, K. Hamer, K. Schulten, J. Koepke, and H. Michel -- Knowledge based structure prediction of the light-harvesting complex II of Rhodospirillum molishianum
  • J. Kostrowicki and H. A. Scheraga -- Some approaches to the multiple-minima problem in protein folding
  • P. Androulakis and C. A. Floudas -- A deterministic global optimization approach for the protein folding problem
  • J. J. Moré and Z. Wu -- \(\varepsilon\)-optimal solutions to distance geometry problems via global continuation
  • R. Pachter, Z. Wang, J. A. Lupo, S. B. Fairchild, and B. Sennett -- The design of chromophore containing biomolecules
  • A. T. Phillips, J. B. Rosen, and V. H. Walke -- Molecular structure determination by convex global underestimation of local energy minima
  • A. Šali, E. Shakhnovich, and M. Karplus -- Thermodynamics and kinetics of protein folding
  • G. Ramachandran and T. Schlick -- Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model
  • M. Vieth, A. Kolinski, C. L. Brooks III, and J. Skolnick -- A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants
  • G. L. Xue, A. J. Zall, and P. M. Pardalos -- Rapid evaluation of potential energy functions in molecular and protein conformations
  • M. M. Zacharias and D. G. Vlachos -- Simulated annealing calculations for optimization of nanoclusters: The roles of quenching, nucleation, and isomerization in cluster morphology
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