Protein Folds
A Distance-Based Approach

Table of Contents

Introduction, H. Bohr and S. Brunak
Overview
Three Paradoxes of Protein Folding, P.G. Wolynes
Protein-Ligand Complexes and Protein Biosynthesis
Conserved Water Molecules and Protein Folding in Fungal Peroxidases, S. Larsen and J.F.W. Petersen
Interplay between Metal Coordination Geometry and Protein Structure, R. Bauer, M. Bjerrum, E. Danielsen, E. Friis, J.M. Hammerstad, L. Hemmingsen, M.V. Pedersen, and J. Ulstrup
Elongation Factor Tu: A G-Protein in Protein Biosynthesis, P. Nissen, M. Kjeldgaard, S. Thirup, L. Reshetnikova, G. Polekhina, B.F.C. Clark and J. Nyborg
Electron Transfer of the Di-Heme Protein: Pseudomonas stutzeri cytochrome c4, , J.-J. Karlsson, A. Kadziola, A. Rasmussen, T.E. Rostrup, and J. Ulstrup
Profile Methods for Protein Structure and Fold Determination
Sequence Matching in Homology Modelling, M. Gribskov
Screening Genome Sequences for Known Folds, M. Braxenthaler and M.J. Sippl
Protein Fold Determination Using a Small Number of Distance Restraints, A. Aszódi, M.J. Gradwell, and W.R. Taylor
How Many Protein Fold Classes Are To Be Found?, P-A. Lindgård and H. Bohr
Distance-Based Protein Structure Prediction and Evaluation
The Effect of a Distance-Cutoff on the Performance of The Distance Matrix Error When Used as a Potential Function to Drive Conformational Search, S. Le Grand, A. Elofsson, and D. Eisenberg
Protein Structure Prediction: How Self-Misleading Can Be Avoided, A. Ya. Badretdinov, A.M. Gutin, and A.V. Finkelstein
Sequence Space Analysis: Identification of Functionally or Structurally Important Residues in Protein Sequence Families, G. Casari, C. Sander, and A. Valencia
Fitting 1-D Predictions into 3-D Structures, B. Rost
Determination of Membrane Bound Protein Structure and Function
Modelling a-helical Integral Membrane Proteins, D. Donnelly and J.B.C. Findlay
Use of Small Organic Compounds and Metal-ions as Structural and Functional Probes in 7TM Receptors, T.W. Schwartz, C.E. Elling, S.M. Nielsen, K. Thirstrup, S. Zoffmann, M. Rosenkilde, D. Marchal, R. den Hollander, U. Gether, and S.A. Hjorth
Using Sequence Information and Model Building to Explore Subtype Specificity in GPCRs, R. Bywater, G. Vriend, L. Oliveira, and D. van Aalten
Statistical Mechanics and Kinetics of Protein Folding Processes
Proposed Rules of the Protein Folding Game, M. Crippen and V.N. Maiorov
Protein Folding Studied by Monte Carlo Simulations, A. Sali, E. Shakhnovich, and M. Karplus
Folding Kinetics of Protein Like Heteropolymers, N.D. Socci and J.N. Onuchic
Energy Landscape and Folding Mechanisms in Proteins, Z. Guo and D. Thirumalai
Topological Aspects of Protein Folds
Resonator Driven Protein Folding: The Implication of Topology for Protein Structure and Folding, J. Bohr, H. Bohr, and S. Brunak
Chirality in Protein Structure, T.W.F. Slidel and J.M. Thornton
Packing within and between Subunits Defined by Internal Cavities, S.J. Hubbard and P. Argos
Protein Modelling and Docking
Modelling and Predicting a-helical Transmembrane Structures, W.R. Taylor and D.T. Jones
HIV GP120 Docking Interactions and Inhibitor Design Based on an Atomic Structure Derived by Molecular Modelling Using the DREIDING II Force Field, J.L. Gabriel and W.M. Mitchell
A Model of the 3D Structure of Obelin-The Photoprotein From Obelia longissima, T. Sandalova
Index