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S. B. Rafi, B. R. Hearn, P. Vedantham, M. P. Jacobson, and A. R. Renslo. "Predicting and improving the membrane permeability of peptidic small molecules", Journal of Medicinal Chemistry, 55 (2012) 3163-3169. [Discussed in SciBX 5 (2012).] Online PMC3325274 P. Kumar, M. Chimenti, H. Pemble, O. Thompson, M. P. Jacobson, and T. Wittmann. "Multisite phosphorylation modulates CLASP-EB1 interactions by disrupting arginine-glutamate salt bridge networks", Journal of Biological Chemistry, 287 (2012) 17050-17064. Online F1000 PMC3366819 C. L. McClendon, L. Hua, G. Barreiro, and M. P. Jacobson. "Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion", Journal of Chemical Theory and Computation, 8 (2012) 2115-2126. Online Simtk PMC3538811 S. S. F. Leung, J. Mijalkovic, K. Borrelli, and M. P. Jacobson. "Testing Physical Models of Passive Membrane Permeation", Journal of Chemical Information and Modeling, 52 (2012) 1621-1636. Online PMC3383340 D. Kuroda, H. Shirai, M. P. Jacobson, and H. Nakamura. "Computer-aided antibody design", Protein Engineering Design Selection, 25 (2012) 507-522. Open Access PMC3449398 A. C. Rand, S. S. F. Leung, H. Eng, C. J. Rotter, R. Sharma, A. S. Kalgutkar, Y. Zhang, M. V. Varma, K. Farley, C. Limberakis, A. M. Mathiowetz, D. A. Price, S. Liras, M. P. Jacobson and R. S. Lokey. "Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance" (invited article). MedChemComm, 3 (2012) 1282-1289. Online E. Dolghih and M. P. Jacobson. "Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein", ACS Chemical Neuroscience, 4 (2013) 361-367. Online C. A. Smith, C. A. Shi, M. K. Chroust, T. E. Bliska, M. J. S. Kelly, M. P. Jacobson, and T. Kortemme. "Design of a Phosphorylatable PDZ Domain with Peptide-Specific Affinity Changes", Structure, 21 (2013) 54-64. Online B. M. Silber, S. Rao, K. L. Fife, A. Gallardo-Godoy, A. R. Renslo, D. K. Dalvie, K. Giles, Y. Freyman, M. Elepano, J. R. Gever, B. Lam, M. P. Jacobson, Y. Huang, L. Z. Benet, S. B. Prusiner. "Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice", Pharmaceutical Research, 30 (2013) 932-950. A. Schonichen, B. A. Webb, M. P. Jacobson, and D. L. Barber. "Considering Protonation as a Post-translational Modification Regulating Protein Structure and Function", Annual Reviews of Biophysics, 42 (2013) 289-314. Eprint J. W. Choy, C. Bryant, C. M. Calvet, P. S. Doyle, S. S. Gunatilleke, S. S. F. Leung, K. K. H. Ang, S. Chen, J. Gut, J. A. Oses-Prieto, J. B. Johnston, M. R. Arkin, A. L. Burlingame, J. Taunton, M. P. Jacobson, J. M. McKerrow, L. M. Podust, and A. R. Renslo. "Chemical-Biological Characterization of a Cruzain Inhibitor Reveals a Second Target and a Mammalian Off-Target". Beilstein J. Org. Chem, 9 (2013) 15-25. PMC3566858 Z. Li, B. M. Silber, S. Rao, J. Gever, C. Bryant, A. Gallardo-Godoy, E. Dolghih, K. Widjaja, M. Elepano, M. P. Jacobson, S. B. Prusiner and A. R. Renslo. "2-Aminothiazoles with Improved Pharmacotherapeutic Properties for Treatment of Prion Disease", ChemMedChem, 8 (2013) 847-857. PMC in progress F. H. Wallrapp, J.-J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson and C. D. Poulter. "Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily". PNAS, 110 (2013) E1196-E1202. Open access PMC3612614 D. Datta, C. L. McClendon, M. P. Jacobson, and J. A. Wells. "Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3", Journal of Biological Chemistry, 288 (2013) 9971-9981. PMC3612614 M. Spreafico and M. P. Jacobson. "In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life", Current Topics in Medicinal Chemistry, 13 (2013) 813-820. Online J. Kim, H. Xiao, X. Tang, C. Kalyanaraman, Y. Patskovsky, P. C. Babbitt, M. P. Jacobson, Y.-S. Lee and S. C. Almo. "PDB to Pathway: structure-guided discovery of carboxy-SAM as a novel metabolite for tRNA wobble base modification", Nature, 498 (2013) 123-126. Online News&Views R. A. Aglietti, S. N. Floor, C. L. McClendon, M. P. Jacobson and J. D. Gross. "Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2", Structure, 21 (2013) 1571-1580. Online C.-H. Choi, B. A. Webb, M. Chimenti, M. P. Jacobson, and D. L. Barber. "A Molecular Mechanism for pH Sensing by FAK in Focal Adhesion Remodelling", J. Cell. Bio., (2013) in press. B. Tian, F. Wallrapp, C. Kalyanaraman, S. Zhao, L. A. Eriksson, and M. P. Jacobson. "Predicting Enzyme-Substrate Specificity with QM/MM Methods: A Case Study of the Stereo-specificity of D-glucarate Dehydratase". Biochemistry, 52 (2013) 5511-5513. Online S. Zhao, R. Kumar, A. Sakai, M. Vetting, B. M. Wood, S. Brown, P. C. Babbitt, S. C. Almo, J. V. Sweedler, J. A. Gerlt, J. E. Cronan, and M. P. Jacobson. "Discovery of new enzymes and metabolic pathways using structure and genome context", Nature, in press. D. Lu, K. Giles, Z. Li, S. Rao, E. Dolghih, J. R. Gever, M. Geva, M. Elepano, A. Oehler, C. Bryant, A. Renslo, M. P. Jacobson, S. J. DeArmond, B. M. Silber, and S. B. Prusiner. "Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice", J. Pharmacol. Exp. Ther., (2013) in press.