1. We have been using homology modeling and simulated annealing in concert with collaborators' NMR and binding-affinity experiments to predict the important intermolecular contacts in the docking of a 14- residue peptide to cyclin dependent kinase 5 (cdk5). A structural model of cdk5 was based on the known structure of a homologous protein, cdk2. Multiple simulated annealing runs are being performed in which the peptide substrate is initially in different orientations. Results of the modeling are being used to suggest site-directed mutations followed by binding assays in an experimental/theoretical attempt to model the cdk5-peptide complex. (With P. Sharma.) 2. We have also introduced a novel empirical term in the potential energy function of the CHARMM program to favor phi-psi conformations observed by solid-state NMR in subsequent computer simulations. The goal is to combine the local but incomplete structural information obtained by solid-state NMR with the CHARMM force field to resolve outstanding questions regarding local protein conformations, such as the structure of loops connecting helices. (With R. Tycko.) 3. The ability to predict molecular structures and detailed dynamical behavior with confidence requires an ongoing systematic evaluation of alternative simulation protocols. For every simulation study, the optimal balance between computational efficiency and physical realism must be evaluated and depends on the particular questions being asked. We continue to study the dependence of simulated structure and dynamics on technical considerations such as the choice of optimization method (e.g., simulated annealing vs. energy minimization, MD vs. MC simulation) and on scientific considerations such as the need to incorporate all relevant molecular interactions (e.g., explicit vs. implicit solvation). We are studying the effects of the protein's environment (hydrated protein, protein in solution, protein in crytal) on the dynamics of myoglobin, a model system for which a wealth of experimental data exist. This study addresses questions of basic biophysical interest as well as helping to characterize different simulation approaches. (With B. Brooks.)