To order through AMS contact the AMS Customer Services Department, P.O. Box 6248, Providence, Rhode Island 02940-6248 USA. For Visa, Mastercard, Discover, and American Express orders call 1-800-321-4AMS.
You may also visit the AMS Bookstore and order directly from there. DIMACS does not distribute or sell these books.
The workshop featured about twenty invited speakers who talked about protein folding, simulation and modeling techniques, heuristics and exact algorithms for globally optimizing nonconvex energy functions. This volume contains a collection of refereed papers from the workshop.
The workshop was sponsored by DIMACS, through grants from the National Science Foundation, the New Jersey Commission on Science and Technology, the National Center for Human Genome Research, the Department of Energy, The National Security Agency, the Centers for Disease Control, The National Institute of Allergy and Infectious Disease, Rutgers University, and other sources. We would like to take this opportunity to thank the sponsors, the DIMACS staff, the participants, the authors, the referees, and the American Mathematical Society, for making the workshop successful and the publication of this volume possible.
Panos M. Pardalos, David Shalloway, and Guoliang Xue
Contents Foreword xi Preface xiii Global minimization on rugged energy landscapes PATRICIA AMARA, JIANPENG MA, AND JOHN E. STRAUB 1 Energy directed conformational search of protein loops and segments ROBERT E. BRUCCOLERI 15 Global optimization methods for protein folding problems RICHARD H. BYRD, ELIZABETH ESKOW, ANDRE VAN DER HOEK, ROBERT B. SCHNABEL, CHUNG-SHANG SHAO, AND ZHIHONG ZOU 29 Tracking metastable states to free-energy global minima BRUCE W. CHURCH, MATEJ ORESIC, AND DAVID SHALLOWAY 41 A multispace search algorithm for molecular energy minimization JUN GU AND BIN Du 65 A minimal principle in the phase problem of X-ray crystallography HERBERT A. HAUPTMAN 89 Knowledge based structure prediction of the light-harvesting complex II of Rhodospirillum molishianum XICHE Hu, DONG Xu, KENNETH HAMER, KLAUS SCHULTEN, JUERGEN KOEPKE, AND HARTMUT MICHEL 97 Some approaches to the multiple-minima problem in protein folding J. KOSTROWICKI AND H. A. SCHERAGA 123 A deterministic global optimization approach for the protein folding problem C. D. MARANAS, I. P. ANDROULAKIS, AND C. A. FLOUDAS 133 E-optimal solutions to distance geometry problems via global continuation JORGE J. MORE AND ZHIJUN WU 151 The design of chromophore containing biomolecules RUTH PACHTER, ZHIQIANG WANG, JAMES A. LUPO, STEVEN B. FAIRCHILD, AND BRIAN SENNETT 169 Molecular structure determination by convex, global underestimation of local energy minima A. T. PHILLIPS, J. B. ROSEN, AND V. H. WALKE 181 Thermodynamics and kinetics of protein folding ANDREJ SALI, EUCENE SHAKHNOVICH, AND MARTIN KARPLUS 199
Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model GOMATHI RAMACHANDRAN AND TAMAR SCHLICK 215 A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants MICHAL VIETH, ANDRZEJ KOLINSKI, C. L. BROOKS, III. AND JEFFREY SKOLNICK 233 Rapid evaluation of potential energy functions in molecular and protein conformations G. L. XUE, A. J. ZALL, AND P. M. PARDALOS 237 Simulated annealing calculations for optimization of nanoclusters: The roles of quenching, nucleation, and isomerization in cluster morphology MARKUS M. ZACHARIAS AND Diosisios G. VLACHOS 251