Protein Folds: A Distance-Based Approach

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. Aszodi, M.J. Gradwell, and W.R. Taylor How Many Protein Fold Classes Are To Be Found?, P-A. Lindgard 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