150.

X. Y. He, Y. J. Li, C. Kalyanaraman, L. L. Qiu, C. Chen, Q. Xiao, W. X. Liu, W. Zhang, J. J. Yang, G. Chen, M. P. Jacobson, and Y. S. Shi.  “GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors”, PNAS, 113 (2016) E5645-E5654.  PMC5035880

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107.

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

94.

J. R. Ingram, S. B. Rafi, L. Lambeth, I. Hsieh, D. Ruelas, K.C. Lim, J. Sakanari, C. S. Craik, M. P. Jacobson and J. H. McKerrow.  “Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni“, PLoS Neglected Tropical Diseases, 6 (2012) e1589.   PMC3317910  F1000

93.

T. Lukk, A. Sakai, C. Kalyanaraman, S. Brown, H. J. Imker, L. Song, A. A. Fedorov, E. V. Fedorov, R. Toro, B. Hillerich, R. Seidel, Y. Patskovsky, M. W. Vetting, S. K. Nair, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson.  “Computational prediction of the diversity of enzyme specificity among dipeptide epimerases in the enolase superfamily”.  PNAS, 109 (2012) 4122-4127. [F1000] [Discussion in PSI/Nature Knowledgebase] [Chemical&Engineering News] PMC3306705

91.

J. M. MacCallum, A. Perez, M. J. Schnieders, L. Hua, M. P. Jacobson, and K. A. Dill.  “Assessment of protein structure refinement in CASP9”.  Proteins, 79 (2011) 74-90.  PMC3238793

83.

J. Nilmeier, L. Hua, E. A. Coutsias, and M. P. Jacobson.  “Assessing protein loop flexibility by hierarchical Monte Carlo sampling”, Journal of Chemical Theory and Computation, 7 (2011) 1562-1574.  PMC3129859

75.

B. D. Sellers, J. P. Nilmeier, and M. P. Jacobson.  “Antibodies as a model system for comparative model refinement”.  Proteins, 78 (2010) 2490-2505.  PMC2998178  Download antibody test set

74.

J. Wilbur, B. D. Sellers, M. P. Jacobson, R. Fletterick, and F. Brodsky.  “Conformation switching of clathrin light chain regulates clathrin lattice assembly”, Developmental Cell, 18 (2010) 841-848.  [‘Issue Highlight’]  Online  PMC2975025  F1000

69.

J. L. McCallum, L. Hua, M. J. Schnieders, V. S. Pande, M. P. Jacobson, and K. A. Dill.  “Assessment of the protein-structure refinement category in CASP8”, Proteins, 77 supplement 9 (2009) 66-80.  PMC2801025

68.

C. J. Farady, B. D. Sellers, M. P. Jacobson, and C. S. Craik.  “Improving the species cross-reactivity of an antibody using computational design”, Bioorganic and Medicinal Chemistry Letters, 19 (2009) 3744-3747.  PMC2724971

67.

E. S. Tan, J. C. Naylor, E. S. Groban, J. R. Bunzow, M. P. Jacobson, D. K. Grandy, and T. S. Scanlan.  “The Molecular Basis of Species-Specific Ligand Activation of Trace Amine-Associated Receptor 1 (TAAR1)”, ACS Chemical Biology, 20 (2009) 209–220.  PMC2677188

64.

T. Schwede, A. Sali, B. Honig, M. Levitt, H. M. Berman, D. Jones, S. E. Brenner, S. K. Burley, R. Das, N. V. Dokholyan, R. L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, C. Humblet, M. P. Jacobson, A. Joachimiak, S. R. Krystek Jr., T. Kortemme, A. Kryshtafovych, G. Montelione, J. Moult, D. Murray, R. Sanchez, T. R. Sosnick, D. M. Standley, T. Stouch, S. Vajda, M. Vasquez, J. D. Westbrook, and I. A. Wilson.  “Outcome of Workshop on Applications of Protein Models in Biomedical Research”, Structure, 13 (2009) 151–159.  PMC2739730

60.

C. Kalyanaraman, H. J. Imker, A. A. Federov, E. V. Federov, M. E. Glasner, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson.  “Discovery of a new dipeptide epimerase enzymatic function guided by homology modeling and virtual screening”, Structure, 16 (2008) 1668–1677.  [Preview:  D. Dunaway-Mariano, “Enzyme Function Discovery“, 16 (2008) 1599–1600.]  Online  PMC2714228

58.

E. S. Tan, E. S. Groban, M. P. Jacobson, and T. S. Scanlan.  “Deciphering the Code to Aminergic G-Protein Coupled Receptor Drug Design.”  Chemistry and Biology, 15 (2008) 343–353.  Online  PMC2713717

55.

S. Wong and M. P. Jacobson.  “In Silico Conformational Selection:  Ligand-Induced Loop Latching”, Proteins, 71 (2008) 153–164.  Online

54.

B. Sellers, K. Zhu, R. A. Friesner, and M. P. Jacobson.  “Towards better refinement of comparative models:  predicting loops in inexact environments”, Proteins, 72 (2008) 959–971.  PMC2764870  Download perturbed loop test set

52.

L. Song, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, S. Brown, P. C. Babbitt, S. C. Almo, M. P. Jacobson, and J. A. Gerlt.  “Assignment and Prediction of Function in the Enolase Superfamily:  A Divergent N-Succinyl Amino Acid Racemase from Bacillus cereus“, Nature Chemical Biology, 3 (2007) 486–491.  [News&Views:  K. N. Allen, “Form finds function“, Nature Chemical Biology, 3 (2007) 452–453.]   [NIGMS “Biomedical Beat“]  F1000  Online

50.

K. Zhu, M. R. Shirts, R. A. Friesner, and M. P. Jacobson.  “Multiscale Optimization of a Truncated Newton Minimization Algorithm and Applications to Proteins and Protein-Ligand Complexes”, Journal of Chemical Theory and Computation, 3 (2007) 640–648.  Online

47.

Z. Xiang, P. J. Steinbach, M. P. Jacobson, R. A. Friesner, and B. Honig.  “Prediction of Side-Chain Conformations on Protein Surfaces”, Proteins, 66 (2007) 814–823.  Online  PMC2743384

44.

X. Li, M. P. Jacobson, K. Zhu, S. Zhao, and R. A. Friesner.  “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, 66 (2007) 824–837.  Online  Pubmed

43.

M. E. Glasner, N. Fayazmanesh, R. Chiang, A. Sakai, M. P. Jacobson, J. A. Gerlt, P. C. Babbitt.  “Evolution of Structure and Function in the o-Succinylbenzoate Synthase/N-Acylamino Acid Racemase Family of the Enolase Superfamily.”  Journal of Molecular Biology, 360 (2006) 228–250.  Online

42.

E. S. Groban, A. Narayanan, and M. P. Jacobson. “Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation”, PLOS Computational Biology, 2 (2006) 238–250.  Online  PMC1440919

40.

V. Kenyon, I. Chorny, T. R. Holman, and M. P. Jacobson. “Novel human lipoxygenase inhibitors discovered using virtual screening with homology models”, Journal of Medicinal Chemistry, 49 (2006) 1356–1363.  Online

30.

E. A. Coutsias, C. L. Seok, M. P. Jacobson, and K. A. Dill.  “A Kinematic View of Loop Closure”, Journal of Computational Chemistry, 25 (2004) 510–528.  Online

29.

V. Guallar, M. P. Jacobson, A. McDermott, and R. A. Friesner. “Computational Modeling of the Catalytic Reaction in Triose Phosphate Isomerase”, Journal of Molecular Biology, 337 (2004) 227–239.

28.

X. Li, M. P. Jacobson, and R. A. Friesner. “High Resolution Prediction of Protein Helix Positions and Orientations”, Proteins, 55 (2004) 368–382.  Online

27.

M. P. Jacobson, D. L. Pincus, C. S. Rapp, T. J. F. Day, B. Honig, D. E. Shaw, and R. A. Friesner. “A Hierarchical Approach to All-Atom Loop Prediction”, Proteins, 55 (2004) 351–367.  F1000  Pubmed

26.

M. Andrec, Y. Harano, M. P. Jacobson, R. A. Friesner, and R. M. Levy. “Complete Protein Structure Determination Using Backbone Residual Dipolar Couplings and Sidechain Rotamer Prediction”, Journal of Structural and Functional Genomics, 2 (2002) 103–111.

25.

M. P. Jacobson, G. A. Kaminski, R. A. Friesner, and C. S. Rapp.  “Force Field Validation Using Protein Side Chain Prediction”, Journal of Physical Chemistry B, 106 (2002) 11673–11680.  Online

24.

M. P. Jacobson, R. A. Friesner, Z. Xiang, and B. Honig. “On the Role of Crystal Packing in Determining Protein Side Chain Conformations”, Journal of Molecular Biology, 320 (2002) 597–608.  F1000