Selected publications, all recent years:

Rapp, C.; Kalyanaraman, C.; Schiffmiller, A.; Schoenbrun, E.L.; Jacobson, M.P.,  “A molecular mechanics approach to modeling protein–ligand interactions: Relative binding affinities in congeneric series,” J. Chem. Inf. Model., 2011, 51, 1634-47.

Wu, D.; Wang, Q.; Assary, R.S.; Broadbelt, L.J.; Krilov, G., “A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate,” J. Chem. Inf. Model., 2011, 51, 1634-47.

Goldfeld, D.A.; Zhu, K.; Beuming, T.; Friesner, R.A., "Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors," PNAS, 2011, ASAP.

Yoo, J.; Medina-Franco, J.L., "Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase," J. Comput. Aided Mol. Des., 2011, 25, 555-567.

Du, J.; Sun, H.; Xi, L.; Li, J.; Yang, Y.; Liu, H.; Yao, X., "Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and Prime/MM-GBSA calculation," J. Comp. Chem., 2011, 13, 2800-2809.

Tron, C.; Cherrier, M.V.; Amara, P.; Martin, L.; Fauth, F.; Fraga, E. et al., "Further Characterization of the [Fe-Fe]-Hydrogenase Maturase  HydG," Eur. J. Inorg. Chem., 2011, 7, 1121–1127.

McRobb, F. M.; Capuano, B.; Crosby, I. T.; Chalmers, D. K.; Yuriev, E., "Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors," J. Chem. Inf. Model., 2010, 50, 626–637.

Rossi, K. A.; Nayeem, A.; Weigelt, C. A.; Krystek Jr., S. R., "Closing the side-chain gap in protein loop modeling," J. Comput. Aided Mol. Des., 2009, 23, 411-418.

Knight, J. L.; Zhou, Z.; Gallicchio, E.; Himmel, D. M.; Friesner, R. A.; Arnold, E.; Levy, R. M., "Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling," Acta Crystallogr., Sect. D: Biol. Crystallogr., 2008, 64, 383-396.

Sellers, B. D.; Zhu, K.; Zhao, S.; Friesner, R. A.; Jacobson, M. P.; "Towards better refinement of comparative models: predicting loops in inexact environments," Proteins, 2008, 72, 959-971.

Rossi, K. A.; Weigelt, C. A.; Nayeem, A.; Krystek, S. R., Jr, "Loopholes and missing links in protein modeling," Protein Sci., 2007, 16, 1999-2012.

Song, L.; Kalyanaraman, C.; Federov, A. A.; Federov, E. V.; Glasner, M. E.; Brown, S.; Babbitt, P. C.; Almo, S. C.; Jacobson, M. P.; Gerlt, J. A., "Prediction and assignment of function for a divergent N-succinyl amino acid racemase," Nature Chemical Biology, 2007, 3, 486-491.

ö  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, 3, 640-648.

ö  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.

ö  Zhu, K.; Shirts, M. R.; and Friesner, R. A., "Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects," J. Chem. Theory Comput., 2007, 3, 2108-2119.

ö  Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A., "Long Loop Prediction Using the Protein Local Optimization Program", Proteins: Structure, Function, and Bioinformatics, 2006, 65, 438-452.

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.

Huang, N.; Kalyanaraman, C.; Bernacki, K.; Jacobson, M. P., "Molecular mechanics methods for predicting protein-ligand binding", Phys. Chem. Chem. Phys., 2006, 8, 5166-5177.

Rezai, T.; Bock, J. E.; Vong, M.; Lokey, R. S.; Jacobson, M. P., "Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: Successful in silico prediction of the relative permeabilities of cyclic peptides", J. Am. Chem. Soc, 2006, 128, 14073-14080.

Lyne, P. D.; Lamb, M. L.; Saeh, J. C., "Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring", J. Med. Chem., 2006, 49, 4805-4808.

ö  Yu, Z.; Jacobson, M. P.; Friesner, R. A., "What role do surfaces play in GB models? A new generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules", J. Comp. Chem., 2006, 27, 72-89.

ö  Yu, Z.; Jacobson, M. P.; Josovitz, J.; Rapp, C. S.; Friesner, R. A., "First-Shell Solvation of Ion Pairs: Correction of Systematic Errors in Implicit Solvent Models", J. Phys. Chem. B., 2004, 108, 6643-6654.

ö  Guallar, V.; Jacobson, M. P.; McDermott, A.; Friesner, R. A., "Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase", J. Mol. Biol., 2004, 337, 227-239.

ö  Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J. F.; Honig, B.; Shaw, D. E.; Friesner, R. A., "A Hierarchical Approach to All-Atom Protein Loop Prediction", Proteins: Structure, Function and Bioinformatics, 2004, 55, 2, 351-367.

ö  Jacobson, M. P.; Kaminski, G. A.; Friesner, R. A; Rapp, C. S., "Force Field Validation Using Protein Side Chain Prediction", J. Phys. Chem. B., 2002, 106, 11673-11680.

ö  Andrec, M.; Harano, Y.; Jacobson, M. P.; Friesner, R. A; Levy, R. M., "Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer predication", J. of Structural and Functional Genomics, 2002, 2, 103-111.