Below are recently published papers highlighting applications using Schrödinger software:
Zhu, K.; Shirts, M. R.; Friesner, R. A.; Jacobson, M. P., "Multiscale Optimization of a Truncated Newton Minimizer and Application to Proteins and Protein-Ligand Complexes", J. Chem. Theory Comput., 2007, ASAP Web Release Date: 14-Feb-2007.
Li, X.; Jacobson, M. P.; Zhu, K.; Zhao, S.; Friesner, R. A., "Assignment of Polar States for Protein Amino Acid Residues Using an Interaction Cluster Decomposition Algorithm and its Application to High Resolution Protein Structure Modeling", Proteins: Structure, Function, and Bioinformatics, 2007, 66, 824-837.
Rummey, C.; Metz, G., "Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site", Proteins: Structure, Function, and Bioinformatics, 2007, 66, 160-171.
Groban, E. S.; Narayanan, A.; Jacobson, M. P., "Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation", PLoS Computational Biology, 2006, 2, 238-250.