Showing papers by "Alain Laederach published in 2006"
TL;DR: The paradoxical observations of extensive native structure within the misfolded species but slow conversion of this species to the native state are readily reconciled by a model in which the mis Folded state is a topological isomer of thenative state, and computational results support the feasibility of this model.
94 citations
TL;DR: This study provides a template for the systematic analysis of the time-evolution of RNA structure from ensembles of local measures that will illuminate the chemical and physical characteristics of each step in the process.
46 citations
01 Jan 2006
TL;DR: The combination of a genetic conformational search algorithm coupled with a novel empirically derived free energy function specific for carbohydrates allows the prediction of free energies of formation to 1 kcal-mol.
Abstract: Automated docking of small molecules to proteins is a powerful approach for both predicting and understanding the molecular mechanisms of ligand recognition and specificity. Carbohydrate recognition is a key component of many biological processes including innate immunity, metabolism, and immune response. Computational tools specific for studying the molecular basis of carbohydrate recognition have recently been developed that efficiently and accurately dock a flexible carbohydrate to a protein. Two aspects of carbohydrate docking are particularly challenging; parametrization of a the potential energy function for the intra-and intermolecular forces and efficient conformational searching. The combination of a genetic conformational search algorithm coupled with a novel empirically derived free energy function specific for carbohydrates allows the prediction of free energies of formation to 1 kcal-mol"' . This chapter covers the basic principles of empirical free energy functions and their application to carbohydrates.