PUBLICATIONS

Matthew P. Jacobson

 

 

PEER-REVIEWED PUBLICATIONS:

 

1.              R. W. Field, J. P. O'Brien, M. P. Jacobson, S. A. B. Solina, W. F. Polik, and H. Ishikawa. "Intramolecular Dynamics in the Frequency Domain", Advances in Chemical Physics, 101 (1997) 463–490.  PDF

2.              M. P. Jacobson, S. L. Coy, and R. W. Field. "Extended Cross Correlation: A Technique for Spectroscopic Pattern Recognition", Journal of Chemical Physics, 107 (1997) 8349–8356.

3.              S. L. Coy, M. P. Jacobson, and R. W. Field. "Identifying Patterns in Multicomponent Signals by Extended Cross Correlation", Journal of Chemical Physics, 107 (1997) 8357–8369.

4.              J. P. O'Brien, M. P. Jacobson, J. J. Sokol, S. L. Coy, and R. W. Field.  "Numerical Pattern Recognition in Acetylene Dispersed Fluorescence Spectra", Journal of Chemical Physics, 108 (1998) 7100–7113.

5.              M. P. Jacobson, J. P. O'Brien, R. J. Silbey, and R. W. Field. "Pure Bending Dynamics in the Acetylene X State up to 15,000 cm-1 of Internal Energy", Journal of Chemical Physics, 109 (1998) 121–133. 

6.              M. P. Jacobson, J. P. O'Brien, and R. W. Field.  "Anomalously Slow Intramolecular Vibrational Redistribution in the Acetylene X State Above 10,000 cm-1 of Internal Energy", Journal of Chemical Physics, 109 (1998) 3831–3840.

7.              M. P. Jacobson, R. J. Silbey, and R. W. Field. "Local Mode Behavior in the Acetylene Bending System", Journal of Chemical Physics, 110 (1999) 845–859. 

8.              E. R. Jamieson, M. P. Jacobson, C. S. Chow, C. M. Barnes, and S. J. Lippard. "Fluorescence Resonance Energy Transfer Study of the Interaction of HMG1 Domain B with Cisplatin-Modified DNA", Journal of Biological Chemistry, 274 (1999) 12346–12354. 

9.              M. P. Jacobson, C. Jung, H. S. Taylor, and R. W. Field, "State-by-State Assignment of the Bending Spectrum of Acetylene at 15000 cm-1: A Case Study of Quantum-Classical Correspondence", Journal of Chemical Physics, 111 (1999) 600–618. 

10.           M. P. Jacobson, S. L. Coy, R. W. Field, S. J. Lipson, R. B. Lockwood, P. S. Armstrong, D. L. Vititoe, and W. A. M. Blumberg, "Pattern Recognition Analysis of CO Atmospheric Simulation Experiments", Journal of Physical Chemistry A, 104 (2000) 249–257. [Winner of the Air Force Research Laboratory, Space Vehicles Directorate "Team Publication of the Year Award" for the year 2000.] 

11.           D. B. Moss, Z.-C. Duan, M. P. Jacobson, J. P. O'Brien, and R. W. Field. "Observation of Coriolis Coupling Between n2+4n4 and 7n4 in Acetylene X1Sg+ by Stimulated Emission Pumping", Journal of Molecular Spectroscopy, 199 (2000) 265–274. 

12.           M. P. Jacobson and R. W. Field.  "Acetylene at the Threshold of Isomerization" (Feature Article), Journal of Physical Chemistry A, 104 (2000) 3073–3086. 

13.           M. P. Jacobson and R. W. Field. "Expectation Values of Resonance Operators", Chemical Physics Letters, 320 (2000) 553–560. 

14.           A. F. Ruckstuhl, M. P. Jacobson, R. W. Field, and J. A. Dodd.  "Baseline Subtraction using Local Robust Regression Estimation", Journal of Quantitative Spectroscopy and Radiative Transfer, 68 (2001) 179–193.

15.           M. P. Jacobson and M. S. Child. "Spectroscopic Signatures of Bond-Breaking Internal Rotation. I. Saddle Point Induced Polyad Breaking", Journal of Chemical Physics, 114 (2001) 250–261. 

16.           M. P. Jacobson and M. S. Child. "Spectroscopic Signatures of Bond-Breaking Internal Rotation. II. Quantum Monodromy and Coriolis Coupling in HCP", Journal of Chemical Physics, 114 (2001) 262–275. 

17.           C. Jung, H. S. Taylor, and M. P. Jacobson. "The Acetylene Bending Spectrum at ~10,000 cm-1: Quantum Assignments in the Midst of Classical Chaos", Journal of Physical Chemistry A, 105 (2001) 681–693. 

18.           M. P. Jacobson and M. S. Child. "Resonant Vibrational Dynamics at a Saddle Point: Scaling Rules for a Zeroth Order Pendulum Model", Journal of Physical Chemistry A, 105 (2001) 2834–2841. 

19.           K. Hoshina, A. Iwasaki, K. Yamanouchi, M. P. Jacobson, and R. W. Field. "High Resolution IR-UV Dispersed Fluorescence Spectrum of Acetylene: New Classes of Bright States", Journal of Chemical Physics, 114 (2001) 7424–7442. 

20.           M. L. Silva, M. P. Jacobson, Z. Duan, and R. W. Field. "Anomalous Simplicity of the A → X Dispersed Fluorescence Spectrum of 13C2H2", Journal of Molecular Structure, 565–566 (2001) 87–91.

21.           M. S. Child, M. P. Jacobson, and C. D. Cooper. "Scaling Laws for Strongly Anharmonic Vibrational Matrix Elements", Journal of Physical Chemistry A, 105 (2001) 10791–10799.

22.           M. L. Silva, M. P. Jacobson, Z. Duan, and R. W. Field. "Unexpected Simplicity in the S1S0 Dispersed Fluorescence Spectrum of 13C2H2", Journal of Chemical Physics, 106 (2002) 7939–7947. 

23.           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

24.           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

25.           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.

26.           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

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

28.           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.

29.           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

30.           Z. Yu, M. P. Jacobson, C. S. Rapp, and R. A. Friesner.  "First-Shell Solvation of Ion Pairs:  Correction of Systematic Errors in Implicit Solvent Models".  Journal of Physical Chemistry B, 108 (2004) 6643–6654.  Online

31.           V. C. Ruddat, R. Mogul, I. Chorny, C. Chen, N. Perrin, S. Whitman, V. Kenyon, M. P. Jacobson, C. F. Bernasconi, and T. R. Holman. "Tryptophan 500 and Arginine 707 Define Product and Substrate Active Site Binding in Soybean Lipoxygenase-1", Biochemistry, 43 (2004) 13063–13071.  Online

32.           C. Kalyanaraman, K. Bernacki, and M. P. Jacobson. "Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes", Biochemistry, 44 (2005) 2059–2071.  [One of top 20 most accessed articles in Biochemistry in 2005.]  Online

33.           S. Wong, K. Bernacki, and M. P. Jacobson. "Competition Between Intramolecular Hydrogen Bonds and Solvation in Phosphorylated Peptides: Simulations with Implicit and Explicit Solvent", Journal of Physical Chemistry B, 109 (2005) 5249–5258.  Online

34.           K. Bernacki, C. Kalyanaraman, and M. P. Jacobson.  "Virtual ligand Screening against E. coli Dihydrofolate Reductase:  Improving Docking Enrichment Using Physics-Based Methods" (invited paper), Journal of Biomolecular Screening, 10 (2005) 675–681.  Online

35.           I. Chorny, K. A. Dill, and M. P. Jacobson. "Surfaces Affect Ion Pairing", Journal of Physical Chemistry B, 109 (2005) 24056–24060.  Online

36.           Z. Yu, M. P. Jacobson, and R. A. Friesner.  "What role do surfaces play in GB models? A new generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules", Journal of Computational Chemistry, 27 (2006) 72–89.  Online  PMC2743414

37.           N. Huang, C. Kalyanaraman, J. J. Irwin, and M. P. Jacobson.  "Physics-Based Scoring of Protein-Ligand Complexes:  Enrichment of Known Inhibitors in Large-Scale Virtual Screening", Journal of Chemical Information and Modeling, 46 (2006) 243–253.  Online

38.           W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner, and R. Farid. "Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects", Journal of Medicinal Chemistry, 49 (2006) 534–553.  [#3 most cited article in J Med Chem in 2006]  Online

39.           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

40.           T. Rezai, B. Yu, G. L. Millhauser, M. P. Jacobson, and R. S. Lokey. "Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers", JACS, 128 (2006) 2510–2511.  Online

41.           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

42.           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

43.           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) 824837.  Online

44.           N. Huang, C. Kalyanaraman, K. Bernacki, and M. P. Jacobson.  "Molecular Mechanics Methods for Predicting Protein-Ligand Binding" (invited feature article), Physical Chemistry Chemical Physics, 8 (2006) 5166–5177.  [PCCP "hot paper"; top downloaded papers in 2006.]  Online

45.           T. Rezai, J. E. Bock, M. Vong, C. Kalyanaraman, R. S. Lokey, and M. P. Jacobson.  "Conformational Flexibility, Internal Hydrogen Bonding, and Passive Membrane Permeability:  Successful In Silico Prediction of the Relative Permeabilities of Cyclic Peptides", JACS, 128 (2006) 14073–14080.  Online

46.           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) 814823.  Online  PMC2743384

47.           D. J. Mandell, I. Chorny, E. S. Groban, S. Wong, E. Levine, C. S. Rapp, and M. P. Jacobson.  "The Strengths of Hydrogen Bonds Involving Phosphorylated Amino Acid Side Chains", JACS, 129 (2007) 820827.  Online

48.           J. Srivastava, D. L. Barber, and M. P. Jacobson.  "Regulation of Cell Processes by pH" (invited article), Physiology, 22 (2007) 3039.  Online

49.           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

50.           N. Huang and M. P. Jacobson.  "New Physics-Based Methods for Studying Protein-Ligand Interactions", Current Opinion in Drug Discovery & Development, 10 (2007) 325-331.

51.           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) 486491.  [News&Views:  K. N. Allen, "Form finds function", Nature Chemical Biology, 3 (2007) 452453.]   [NIGMS "Biomedical Beat"]  F1000  Online

52.           C. Kalyanaraman and M. P. Jacobson.  "An atomistic model of passive membrane permeability:  Application to a series of FDA approved drugs", Journal of Computer-Aided Molecular Design, 21 (2007) 675679.  Online

53.           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

54.           S. Wong and M. P. Jacobson.  "In Silico Conformational Selection:  Ligand-Induced Loop Latching", Proteins, 71 (2008) 153164.  Online

55.           A. P. Graves, D. M. Shivakumar, S. E. Boyce, M. P. Jacobson, D. A. Case, and B. K. Shoichet.  "Rescoring docking hit lists for model cavity sites: predictions and experimental testing", Journal of Molecular Biology, 377 (2008) 914–934.  Online  PMC2752715

56.           J. Nilmeier and M. P. Jacobson.  "Multiscale Monte Carlo Sidechain Sampling:  Application to Binding Pocket Flexibility", Journal of Chemical Theory and Computation, 4 (2008) 835–846.

57.           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

58.           J. Srivastava, G. Barreiro, S. Groscurth, A. R. Gingras, B. T. Goult, D. R. Critchley, M. J. S. Kelly, M. P. Jacobson, and D. L. Barber.  "Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling".  PNAS, 105 (2008) 1443614441.  Online  PMC2532973

59.           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

60.           C. Frantz, G. Barreiro, L. Dominguez, X. Chen, R. Eddy, J. Condeelis, M. J. S. Kelly, M. P. Jacobson and D. L. Barber.  "Cofilin is a pH Sensor for Actin Free Barbed End Formation".  Journal of Cell Biology, 183 (2008) 865–879.  ["In this issue":  "Cofilin activity is a total coincidence", Journal of Cell Biology, 183 (2008) 753.]  Online  PMC2592832  F1000

61.           U. Pieper, R. Chiang, J. J. Seffernick, S. D. Brown, M. E. Glasner, L. Kelly, N. Eswar, M. Sauder, S. K. Burley, S. Almo, J. A. Gerlt, F. Raushel, B. K. Shoichet, M. P. Jacobson, P. C. Babbitt, A. Sali.  "Target Selection and Annotation for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies", Journal of Structural and Functional Genomics, 10 (2009) 107–125.  PMC2693957

62.           C. S. Rapp, C. Schonbrun, M. P. Jacobson and Niu Huang.  "Automated Site Preparation in Rescoring of Receptor Ligand Complexes", Proteins, 77 (2009) 52-61.  PMC2744578

63.           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

64.           A. Narayanan, B. D. Sellers, and M. P. Jacobson.  "Energy-based analysis and prediction of the orientation of antibody heavy and light chain variable domains", Journal of Molecular Biology, 388 (2009) 941–953.

65.           A. Narayanan and M. P. Jacobson.  "Computational studies of protein regulation by post-translational phosphorylation", Current Opinion in Structural Biology, 19 (2009) 156–163.

66.           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

67.           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

68.           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

69.           J. F. Rakus, C. Kalyanaraman, A. A. Fedorov, Elena V. Fedorov, F. P. Mills-Groninger, K. Bain, J. M. Sauder, S. K. Burley, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. "Computation Facilitated Assignment of Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis", Biochemistry, 48 (2009) 11546-58.  PMC2787699

70.           J. Nilmeier and M. P. Jacobson.  "Monte Carlo sampling with hierarchical move sets:  POSH Monte Carlo", JCTC, 5 (2009) 1968-1984.  PMC2612633

71.           C. L. McClendon, G. Friedland, D. L. Mobley, H. Amirkhani, and M. P. Jacobson.  "Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles", Journal of Chemical Theory and Computation, 5 (2009) 2486-2502.  PMC2790287

72.           C.-K. Chen, S. S. F. Leung, C. Guilbert, M. P. Jacobson, J. H. McKerrow, and L. M. Podust.  "Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole".  PLoS Neglected Tropical Diseases, 4 (2010) e651.  PMC2850312

73.           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.  [ďIssue HighlightŇ]  Online  PMC2975025  F1000

74.           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

75.           N. Huang and M. P. Jacobson.  "Virtual Fragment Screening for Binding Site Assessment", PLoS One, 5 (2010) e10109.  PMC2852417

76.           P. S. Doyle, C.-K. Chen, J. B. Johnston, S. Hopkins, S. S. F. Leung, M. P. Jacobson, J. C. Engel, J. H. McKerrow, L. M. Podust. "A Non-azole CYP51 Inhibitor Cures Chagas Disease in a Mouse Model of Acute Infection", Antimicrobial Agents and Chemotherapy, 54 (2010) 2480-2488. PMC2876414

77.           C. Kalyanaraman and M. P. Jacobson.  "Studying enzyme-substrate specificity in silico:  A case study of the E. coli glycolysis pathway" (Rapid Report), Biochemistry, 49 (2010) 4003-4005.  PMC2877507

78.           T. Shimazu, M. D. Hirschey, L. Hua, B. Schwer, D. B. Lombard, Y. Li, J. Bunkenborg, F. W. Alt, M. P. Jacobson, and E. Verdin.  "SIRT3 Deacetylates Mitochondrial 3-Hydroxy-3-Methylglutaryl CoA Synthase 2, Increases its Enzymatic Activity and Regulates Ketone Body Production".  Cell Metabolism, 12 (2010) 654-661.  Online  PMC3310379

79.           F. Morcos, S. Chatterjee, C. L. McClendon, P. R. Brenner, R. Lopez-Rendon, J. Zintsmaster, M. Ercsey-Ravasz, C. R. Sweet, M. P. Jacobson, J. W. Peng, and J. A. Izaguirre.  "Modeling the conformational ensembles of NMR relaxation dispersion: molecular dynamics study of slow functional motions in the Pin1-WW domain".  PLoS Computational Biology, 6 (2010) e1001015.  PMC2996313

80.           S. Wong, B. D. Sellers, and M. P. Jacobson.  "Effects of Somatic Mutations on CDR Loop Flexibility During Affinity Maturation", Proteins, 79 (2011) 821-829.  Online

81.           J. D. Sadowsky, M. A. Burlingame, D. W. Wolan, C. L. McClendon, M. P. Jacobson and J. A. Wells.  "Turning a protein kinase (PDK1) on or off from a single allosteric site via disulfide trapping".  PNAS, 108 (2011) 6056-6061.  PMC21430264

82.           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

83.           B. C. Cossins, M. P. Jacobson, and V. Guallar.  "A new view of the bacterial cytosol environment."  PLoS Computational Biology, 7 (2011) e1002066.  PMC3111478

84.           E. Dolghih, C. Bryant, A. R. Renslo, and M. P. Jacobson.  "Predicting binding to P-glycoprotein by flexible receptor docking", PLoS Computational Biology, 7 (2011) e1002083.  PMC3121697

85.           B. A. Webb, M. Chimenti, M. P. Jacobson, and D. L. Barber.  "Dysregulated pH:  A perfect storm for cancer progression" (invited article).  Nature Reviews Cancer, 11 (2011) 671-677.  Online 

86.           T. R. White, C. M. Renzelman, A. C. Rand, T. Rezai, C. M. McEwen, V. M. Gelev, R. A. Turner, A. C. Rand, R. G. Linington, S. S. F. Leung, A. S. Kalgutkar, J. N. Bauman, Y. Zhang, S. Liras, D. A. Price, A. M. Mathiowetz, M. P. Jacobson, and R. S. Lokey. "On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds", Nature Chemical Biology, 7 (2011) 810-817.  PMC3210067.  [Discussed in SciBX 4 (2011).]  F1000

87.           C. S. Rapp, C. Kalyanaraman, A. Schiffmiller, E. L. Schoenbrun, and M. P. Jacobson.  "A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions:  Relative Binding Affinities in Congeneric Series", Journal of Chemical Information and Modeling, 51 (2011) 2082-2089.  PMC3183355

88.           A. Narayanan, L. L. LeClaire, D. L. Barber, and M. P. Jacobson.  "Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation".  PLoS Computational Biology, 7 (2011) e1002226.  PMC3220268

89.           J. A. Gerlt, K. N. Allen, S. C. Almo, R. N. Armstrong, P. C. Babbitt, J. E. Cronan, D. Dunaway-Mariano, H. J. Imker, M. P. Jacobson, W. Minor, C. D. Poulter, F. M. Raushel, A. Sali, B. K. Shoichet, and J. V. Sweedler.  "The Enzyme Function Initiative", Biochemistry, 50 (2011) 9950-9962.  PMC3238057

90.           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

91.           J. A. Gerlt, P. C. Babbitt, M. P. Jacobson, and S. C. Almo.  "Divergent evolution in the enolase superfamily: Strategies for assigning functions" (mini-review).  Journal of Biological Chemistry, 287 (2012) 29-34.  PMC3249080

92.           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]  PMC3306705

93.           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

94.           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

95.           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

96.           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

97.           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

98.           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

99.           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

100.        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

101.        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

102.        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.

103.        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

104.        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

105.        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

106.        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

107.        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

108.        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

109.        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

110.        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 

111.        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.

112.        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

113.        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.

114.        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.   

 

NON-PEER REVIEWED PUBLICATIONS AND OTHER CREATIVE ACTIVITIES:

 

Review Articles

M. P. Jacobson and A. Sali.  "Comparative Protein Structure Modeling and its Application to Drug Discovery".  Annual Reports in Medicinal Chemistry, 39 (2004) 259–276.

 

Books and Chapters

R. N. Zare, B. H. Spencer, D. S. Springer, and M. P. Jacobson. Laser Experiments for Beginners (University Science Books, Sausalito, CA, 1995).

 

Other Publications

M. P. Jacobson. "Review of 'Bioinformatics and Drug Discovery' ".  ChemMedChem, 1 (2006) 654.

Thesis:  Spectroscopic Patterns Encode Unimolecular Dynamics, MIT, 1999.

 

M. P. Jacobson, R. S. Lokey, S. Liras, and J. Liras, editors.  "Designing molecules to cross biological membranes". Current Topics in Medicinal Chemistry (2013).