VOLUME Twenty Three
TITLE: "Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding"
EDITORS: P. M. Pardalos, D. Shalloway, and G. Xue
Published by the American Mathematical Society

Ordering Information

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.

• 1. Preface
• 2. Table of Contents

PREFACE

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
June 1995

TABLE OF CONTENTS

                            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

                                                                     

Index of Volumes

DIMACS Homepage