Publications

Thesis:  "Spectroscopic Patterns Encode Unimolecular Dynamics", MIT, 1999.
  1. R. N. Zare, B. H. Spencer, D. S. Springer, M. P. Jacobson, Laser Experiments for Beginners (University Science Books, Sausalito, CA, 1995).
  2. R. W. Field, J. P. O'Brien, M. P. Jacobson, S. A. B. Solina, W. F. Polik, H. Ishikawa, "Intramolecular Dynamics in the Frequency Domain", Advances in Chemical Physics, 101 (1997), pp. 463-490.
  3. M. P. Jacobson, S. L. Coy, R. W. Field, "Extended Cross Correlation: A Technique for Spectroscopic Pattern Recognition", Journal of Chemical Physics, 107 (1997), pp. 8349-8356.
  4. S. L. Coy, M. P. Jacobson, R. W. Field, "Identifying Patterns in Multicomponent Signals by Extended Cross Correlation", Journal of Chemical Physics, 107 (1997), pp. 8357-8369.
  5. J. P. O'Brien, M. P. Jacobson, J. J. Sokol, S. L. Coy, R. W. Field, "Numerical Pattern Recognition in Acetylene Dispersed Fluorescence Spectra", Journal of Chemical Physics, 108 (1998), pp. 7100-7113.
  6. M. P. Jacobson, J. P. O'Brien, R. J. Silbey, 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), pp. 121-133.
  7. M. P. Jacobson, J. P. O'Brien, 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), pp. 3831-3840.
  8. M. P. Jacobson, R. J. Silbey, and R. W. Field, "Local Mode Behavior in the Acetylene Bending System", Journal of Chemical Physics, 110 (1999), pp. 845-859.
  9. E. R. Jamieson, M. P. Jacobson, C. S. Chow, C. M. Barnes, 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), pp. 12346-12354.
  10. 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), pp. 600-618.
  11. 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, 104 (2000), pp. 249-257. [Winner of the Air Force Research Laboratory, Space Vehicles Directorate "Team Publication of the Year Award" for the year 2000.]
  12. D. B. Moss, Z.-C. Duan, M. P. Jacobson, J. P. O'Brien, and R. W. Field, "Observation of Coriolis Coupling Between v2+4v4 and 7v4 in Acetylene by Stimulated Emission Pumping", Journal of Molecular Spectroscopy, 199 (2000), pp. 265-274.
  13. M. P. Jacobson and R. W. Field, "Acetylene at the Threshold of Isomerization" (Feature Article), Journal of Physical Chemistry A, 104 (2000), pp. 3073-3086.
  14. M. P. Jacobson and R. W. Field. "Expectation Values of Resonance Operators", Chemical Physics Letters, 320 (2000), pp. 553-560.
  15. 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), pp. 179-193.
  16. 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), pp. 250-261.
  17. 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), pp. 262-275.
  18. 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), pp. 681-693.
  19. 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), pp. 2834-2841.
  20. 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), pp. 7424-7442.
  21. 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), pp. 87-91.
  22. M. S. Child, M. P. Jacobson, and C. D. Cooper. "Scaling Laws for Stongly Anharmonic Vibrational Matrix Elements", Journal of Physical Chemistry, 105 (2001), pp. 10791-10799.
  23. M. L. Silva, M. P. Jacobson, Z. Duan, and R. W. Field. "Unexpected Simplicity in the S1-S0 Dispersed Fluorescence Spectra of 13C2H2", Journal of Chemical Physics, 116 (2002), pp. 7939-7947.
  24. M. P. Jacobson, R. A. Friesner, Z. Xiang, and B. Honig. "On the Role of Crystal Packing Forces in Determining Protein Sidechain Conformations", Journal of Molecular Biology, 320 (2002), pp. 597-608.
    25. Faculty of 1000 Recommended Article
  25. M. P. Jacobson, G. A. Kaminski, R. A. Friesner, and C. S. Rapp. "Force Field Validation Using Protein Sidechain Prediction", Journal of Physical Chemistry B, 106 (2002), 11673-11680. Online Request Reprint
  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), pp. 103-111.
  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), pp. 351-367. Supplementary Materials Faculty of 1000 Recommended Article
  28. X. Li, M. P. Jacobson, and R. A. Friesner. "High Resolution Prediction of Protein Helix Positions and Orientations", Proteins, 55 (2004), pp. 368-382. 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), pp. 227-239.
  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), pp. 510-528. Online
  31. 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), pp. 6643-6654. Online
  32. M. P. Jacobson and A. Sali. "Comparative Protein Structure Modeling and Its Applications to Drug Discovery", Annual Reports in Medicinal Chemistry, 39 (2004), pp. 259-276.
  33. 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), pp. 13063-13071. Online
  34. 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), pp. 2059-2071. Online Request Reprint A "Most-Accessed" article in Biochemistry in 2005
  35. 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), pp. 5249-5258. Online Request Reprint
  36. 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), pp. 675-681. Online
  37. I. Chorny, K. A. Dill, and M. P. Jacobson. "Surfaces Affect Ion Pairing", Journal of Physical Chemistry B, 109 (2005), pp. 24056-60. Online Request Reprint
  38. 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), pp. 72-89. Online
  39. N. Huang, C. Kalyanaraman, J. J. Irwin, and M. P. Jacobson. "A Physics-Based Scoring Method Improves Early Enrichment in Virtual Screening of Large Compound databases", Journal of Chemical Information and Modeling, 46 (2006), pp. 243-253. Online Request Reprint
  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), pp. 1356-1363. Online
  41. 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), pp. 534-553. Online Request Reprint A "Most Cited Article in 2006"
  42. 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), pp. 2510-2511. Online
  43. E. S. Groban*, A. Narayanan*, and M. P. Jacobson. "Phosphorylation-Induced Conformational Changes in Protein Loops and Helices", PLOS Computational Biology, 2 (2006), pp. 238-250. (*Joint first authors) Online
  44. M. E. Glasner, N. Fayazmanesh, R. Chiang, A. Sakai, M. P. Jacobson, J. A. Gerlt, and 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), pp. 228-250. Online
  45. M. P. Jacobson. "Review of 'Bioinformatics and Drug Discovery' ", ChemMedChem, 1 (2006), p. 654. Online
  46. 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 (2006), pp. 824-837. Online
  47. N. Huang, C. Kalyanaraman, K. Bernacki, and M. P. Jacobson. "Molecular mechanics methods for predicting protein-ligand binding (invited article)", Physical Chemistry Chemical Physics, 8 (2006), pp. 5166-5177. Online
  48. T. Rezai, J. E. Bock, M. Vong, 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", Journal of the American Chemical Society, 128 (2006), pp. 14073-14080. Online Request Reprint
  49. 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), pp. 814-823. Online
  50. 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", Journal of the American Chemical Society, 129 (2007), pp. 820-827. Online Request Reprint
  51. J. Srivastava, D. L. Barber, and M. P. Jacobson. "Intracellular pH sensors: Design principles and functional significance", Physiology, 22 (2007), pp. 30-39. Online
  52. K. Zhu, M. R. Shirts, R. A. Friesner, and M. P. Jacobson. "Multiscale optimization of a truncated Newton minimizer and applications to proteins and protein-ligand complexes", Journal of Chemical Theory and Computation, 3 (2007), pp. 640. Online
  53. N. Huang and M. P. Jacobson. "Physics-Based Methods for Studying Protein-Ligand Interactions", Current Opinion in Drug Discovery and Development, 10 (2007) pp. 325-331.
  54. S. Wong and M. P. Jacobson. "In Silico Conformational Selection: Ligand-Induced Loop Latching", Proteins, 71 (2007) pp. 153-164. Online
  55. L. Song, C. Kalyanaraman, A. A. Federov, E. V. Federov, M. E. Glasner, S. Brown, P. C. Babbitt, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. "Prediction and assignment of function in the enolase superfamily: A divergent N-succinyl amino acid racemase from Bacillus cereus", Nature Chemical Biology, 3 (2007), pp. 486-491. Online News and Views NIGMS "Biomedical Beat" F1000
  56. 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) pp. 675-679. Online
  57. B. D. Sellers*, K. Zhu*, S. Zhao, R. A. Friesner, M. P. Jacobson. "Towards better refinement of comparative models: predicting loops in inexact environments", Proteins, in press (*Joint first authors) Download perturbed loop test set (12MB)
  58. 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) pp. 914-934.
  59. J. Nilmeier and M. P. Jacobson. "Multiscale Monte Carlo Sidechain Sampling: Application to Binding Pocket Flexibility", Journal of Chemical Theory and Computation, in press.
  60. 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) pp. 343-353.
  61. J. Srivastava, G. Barreiro, S. Groschurth, A. R. Gingras, B. T. Goult, D. R. Critchley, M. J. S. Kelly, M. P. Jacobson, and D. L. Barber. "pH Regulates talin binding to actin for focal adhesion dynamics and cell migration", PNAS, in press.
  62. K. Bernacki and M. P. Jacobson. "A Simple Method to Improve the Quality of Virtual Ligand Screening Against Homology Models: Application to Parasite Cysteine Proteases". Chemical Biology and Drug Design, submitted.