PUBLICATIONS
Matthew P.
Jacobson
PEER-REVIEWED PUBLICATIONS:
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 S1 → S0 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) 824–837. 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) 814–823. 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) 820–827. Online
48. J. Srivastava, D. L. Barber, and M. P. Jacobson. "Regulation of Cell Processes by pH" (invited article), Physiology, 22 (2007) 30–39. 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) 486–491. [News&Views: K. N. Allen, "Form finds function", Nature Chemical Biology, 3 (2007) 452–453.] [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) 675–679. 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) 153–164. 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) 14436–14441. 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
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", JCTC, 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. [ÔIssue HighlightÕ] Online PMC2975025
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
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
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
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
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
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, in press.
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, in press.
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, accepted.
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, in press.
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, in press.
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, accepted.
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, accepted.
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.