1: Tan ES, Naylor JC, Groban ES, Bunzow JR, Jacobson MP, Grandy DK, Scanlan TS. The Molecular Basis of Species-Specific Ligand Activation of Trace Amine-Associated Receptor 1 (TAAR(1)). ACS Chem Biol. 2009 Mar 3. [Epub ahead of print] PMID: 19256523 [PubMed - as supplied by publisher] 2: Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Feb 14. [Epub ahead of print] PMID: 19219566 [PubMed - as supplied by publisher] 3: Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13;17(2):151-9. PMID: 19217386 [PubMed - in process] 4: Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL. Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. J Cell Biol. 2008 Dec 1;183(5):865-79. Epub 2008 Nov 24. PMID: 19029335 [PubMed - indexed for MEDLINE] 5: Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008 Nov 12;16(11):1668-77. PMID: 19000819 [PubMed - indexed for MEDLINE] 6: Srivastava J, Barreiro G, Groscurth S, Gingras AR, Goult BT, Critchley DR, Kelly MJ, Jacobson MP, Barber DL. Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14436-41. Epub 2008 Sep 9. PMID: 18780792 [PubMed - indexed for MEDLINE] 7: Tan ES, Groban ES, Jacobson MP, Scanlan TS. Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol. 2008 Apr;15(4):343-53. PMID: 18420141 [PubMed - indexed for MEDLINE] 8: Elliott JO, Seals BF, Jacobson MP. Osteoprotective knowledge in a multiethnic epilepsy population. J Neurosci Nurs. 2008 Feb;40(1):14-24, 39. PMID: 18330406 [PubMed - indexed for MEDLINE] 9: Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71. PMID: 18300241 [PubMed - indexed for MEDLINE] 10: Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID: 18280498 [PubMed - indexed for MEDLINE] 11: Kalyanaraman C, Jacobson MP. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des. 2007 Dec;21(12):675-9. Epub 2007 Nov 8. PMID: 17989930 [PubMed - indexed for MEDLINE] 12: Wong S, Jacobson MP. Conformational selection in silico: loop latching motions and ligand binding in enzymes. Proteins. 2008 Apr;71(1):153-64. PMID: 17932934 [PubMed - indexed for MEDLINE] 13: Elliott JO, Jacobson MP, Haneef Z. Cardiovascular risk factors and homocysteine in epilepsy. Epilepsy Res. 2007 Sep;76(2-3):113-23. Epub 2007 Aug 21. PMID: 17714918 [PubMed - indexed for MEDLINE] 14: Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID: 17603539 [PubMed - indexed for MEDLINE] 15: Huang N, Jacobson MP. Physics-based methods for studying protein-ligand interactions. Curr Opin Drug Discov Devel. 2007 May;10(3):325-31. Review. PMID: 17554859 [PubMed - indexed for MEDLINE] 16: Elliott JO, Seals BF, Jacobson MP. Use of the Precaution Adoption Process Model to examine predictors of osteoprotective behavior in epilepsy. Seizure. 2007 Jul;16(5):424-37. Epub 2007 Apr 18. PMID: 17446092 [PubMed - indexed for MEDLINE] 17: Srivastava J, Barber DL, Jacobson MP. Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda). 2007 Feb;22:30-9. Review. PMID: 17289928 [PubMed - indexed for MEDLINE] 18: Mandell DJ, Chorny I, Groban ES, Wong SE, Levine E, Rapp CS, Jacobson MP. Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc. 2007 Jan 31;129(4):820-7. PMID: 17243818 [PubMed - indexed for MEDLINE] 19: Xiang Z, Steinbach PJ, Jacobson MP, Friesner RA, Honig B. Prediction of side-chain conformations on protein surfaces. Proteins. 2007 Mar 1;66(4):814-23. PMID: 17206724 [PubMed - indexed for MEDLINE] 20: Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys. 2006 Nov 28;8(44):5166-77. Epub 2006 Sep 1. Review. PMID: 17203140 [PubMed - indexed for MEDLINE] 21: Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. 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. 2007 Mar 1;66(4):824-37. PMID: 17154422 [PubMed - indexed for MEDLINE] 22: Elliott JO, Jacobson MP, Haneef Z. Homocysteine and bone loss in epilepsy. Seizure. 2007 Jan;16(1):22-34. Epub 2006 Nov 15. PMID: 17110134 [PubMed - indexed for MEDLINE] 23: Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, Jacobson MP. 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 Nov 1;128(43):14073-80. PMID: 17061890 [PubMed - indexed for MEDLINE] 24: Elliott JO, Jacobson MP, Seals BF. Self-efficacy, knowledge, health beliefs, quality of life, and stigma in relation to osteoprotective behaviors in epilepsy. Epilepsy Behav. 2006 Nov;9(3):478-91. Epub 2006 Aug 28. PMID: 16935031 [PubMed - indexed for MEDLINE] 25: Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol. 2006 Jun 30;360(1):228-50. Epub 2006 May 11. PMID: 16740275 [PubMed - indexed for MEDLINE] 26: Groban ES, Narayanan A, Jacobson MP. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol. 2006 Apr;2(4):e32. Epub 2006 Apr 21. PMID: 16628247 [PubMed - indexed for MEDLINE]