James
M. Briggs
Publication List
October 13, 2005
72. Mulder, B. A.; Anaya, S.; Yu, P.; Lee, K. W.; Nguyen, A.; Murphy, J.; Willson, R.; Briggs, J. M.;
Gao, X.; Hardin, S. H.
Nucleotide modification at the gamma-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase
Nucleic Acid Res. , 2005,
33(15),4865-73.
71. LeMagueres, P.; Im, H.; Ebalunode, J.; Strych, U.; Benedik, M. J.;
Briggs, J. M; Kohn, H.; Krause K. L. The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis
contains a conserved entryway into the active site Biochemistry , 2005,
44,1471-81.
70. Deng, J.; Lee, K. W.; Sanchez, T.; Cui M.; Neamati, N.;
Briggs, J. M. Dynamic receptor based pharmacophore model development and its application in designing
novel HIV-1 integrase inhibitors J. Med. Chem. , 2005,
48,1496-505.
69. Brigo, A.; Lee, K. W.; Irucu Mustata, G.;
Briggs, J. M. Comparison of multiple molecular dynamics trajectories calculated for the drug resistant HIV-1 integrase
T66I/M154I catalytic domain Biophys. J., 2005,
88,3072-82.
68. Brigo, A.; Lee, K. W.; Fogolari, F; Mustata, G. I.;
Briggs, J. M. Comparitive molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant
: binding modes and drug resistance to a diketo acid Proteins, 2005,
59,723-41.
67. Lee, M. C.; Deng, J.; Briggs, J. M.;
Duan, Y. Large scale conformational dynamics of the HIV-1 integrase core domain and its
catalytic loop mutants Biophys. J., 2005,
88,3133-46.
66. Barreca, M.
L.; Rao, A.; De Luca, L.; Zappalà, M.; Gurnari, C.; Monforte, P.; De Clercq, E.;
Van Maele, B.; Debyser, Z.; Witvrouw, M.; Briggs, J.M.; Chimirri, A. “Efficient 3D Database Screening for Novel
HIV-1 IN Inhibitors”, J. Chem. Inf. Comp. Sci., 2004, in press (Web Release Date:
15-May-2004; (Article) DOI: 10.1021/ci034296e)
65. Mustata, G. I.; Briggs, J. M.
“Cluster Analysis of Water Molecules in Alanine Racemase and their Putative
Structural Role”, Protein
64. Mustata, G. I.; Brigo, A.;
Briggs, J. M. “HIV-1 Integrase Pharmacophore Model Derived from Diverse Classes
of Inhibitors”, Bioorg. Med. Chem. Lett.,
2004, 14, 1447-1454.
63. Adesokan, A. A.; Roberts, V. A.;
Lee, K. W.; Lins, R. D.; Briggs, J. M. “Prediction of HIV-1 Integrase/viral DNA
Interactions in the Catalytic Domain by Fast Molecular Docking”, J. Med. Chem., 2004, 47, 821-8.
62. Mursinna, R. S.; Lee, K. W.;
Briggs, J. M.; Martinis, S. A. “Molecular
Dissection of a Critical Specificity Determinant within the Amino Acid Editing
Domain of Leucyl-tRNA Synthetase”, Biochem.,
2004, 43, 155-165.
61. Lee, K. W.; Briggs, J. M.
“Molecular Modeling Study of the Editing Active Site of Escherichia coli Leucyl-tRNA Synthetase: Two Amino Acid Binding
Sites in the editing domain”, Proteins: Str. Function Bioinformatics, 2004, 54, 693-704.
60. Mustata,
G. I.; Briggs, J. M. “Molecular
Dynamics Studies of Alanine Racemase: A Structural Model for Drug Design”, Biopolymers, 2003, 70, 186-200.
59. Laurents, D. V.;
Huyghues-Despointes, B. M. P.; Bruix, M.; Thurlkill, R. L.; Schell, D.; Newsom,
S.; Grimsley, G. R.; Shaw, K. L.; Treviño, S.; Rico, M.; Briggs, J. M.;
Antosiewicz, J. M.; Scholtz, J. M.; Pace, C. N. “Charge-Charge Interactions are
Key Determinants of the pK values of Ionizable Groups in Ribonuclease Sa
(pI=3.5) and a Basic Variant (pI=10.2)”, J.
Mol. Biol., 2003, 325, 1077-1092.
58. Huyghues-Despointes, B. M. P.;
Thurlkill, R. L.; Daily, M. D.; Schell, D.; Briggs, J. M.; Antosiewicz, J. M.;
Pace, C. N.; Scholtz, J. M. “pK Values of Histidine Residues in Ribonuclease
Sa: Effect of Salt and Net Charge”, J.
Mol. Biol., 2003, 325, 1093-1105.
57. Barreca, M. L.; Lee, K. W.; Chimirri,
A.; Briggs, J. M. “Molecular dynamics studies of the wild-type and double
mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug
resistance”, Biophys. J., 2003,
84, 1450-1463.
56. Mustata, G. I.; Briggs, J. M. “A
Structure-Based Design Approach for the Identification of Novel Inhibitors:
Application to an Alanine Racemase”, J.
Comput.-Aided Mol. Design, 2002,
16, 935-953.
55. Pace, C. N.;
Huyghues-Despointes, B. M. P.; Briggs, J. M.; Scholtz, J. M. “Charge-Charge
Interactions are the Primary Determinants of the pK Values of the Ionizable
Groups in Ribonuclease T1”, Biophys. Chem., 2002, 101-102, 211-219.
54. Cui, M.; Huang, X.; Luo, X.;
Briggs, J. M.; Ji, R.; Chen, K.; Shen, J.; Jiang, H. “Molecular
Docking and 3D-QSAR Studies on Gag Peptide Analogue Inhibitors Interacting with
Human Cyclophilin A”, J. Med. Chem., 2002, 45, 5249-59.
53. Fu, W.; Cui, M.; Briggs, J. M.;
Huang, X.; Xiong, B.; Zhang, Y.; Luo, X.; Shen, J.; Ji, R.; Jiang, H.; Chen, K.
“Brownian Dynamics Simulations of Recognition of the Scorpion Toxin Maurotoxin
with the Voltage-Gated Potassium Ion Channels”, Biophys. J., 2002, 83, 2370-85.
52. Soares, T. A.; Lins, R. D.;
Straatsma, T. P.; Briggs, J. M. “Internal Dynamics and
51. Cui, M.; Wu, J.; Briggs, J. M.;
Fu, W.; Zhang, Y.; Shen, J.; Luo, X.; Chi, Z.; Ji, R.; Jiang, H.; Chen, K.,
“Brownian Dynamics Simulations of the Recognition of the Scorpion Toxin
P05 with the Small Conductance Calcium-activated Potassium Channels”, J.
Mol. Biol., 2002, 318, 417-28.
50.
Huang H.-C.; Briggs, J. M. “The Association Between a Negatively Charged Ligand
and the Electronegative Binding Pocket of its Receptor”, Biopolymers, 2002,
63, 247-260.
49.
Ondrechen, M. J.; Briggs, J. M.; McCammon, J. A. “A Model for Enzyme-Substrate
Interaction in Alanine Racemase”, J. Am. Chem. Soc., 2001, 123,
2830-2834.
48.
Cui M.; Shen J.; Briggs, J. M.; Luo X.; Tan X.; Jiang H.; Chen K.; Ji L.
“Brownian Dynamics Simulations of Interaction Between Scorpion Toxin Lq2 and
Potassium Ion Channel”, Biophys. J., 2001, 80, 1659-69.
47.
Lee, K. W.; Briggs, J. M. “Comparative Molecular Field Analysis (CoMFA) Study
of Epothilones as Tubulin Inhibitors: Pharmacophore Search Using 3D QSAR
Methods”, J. Computer-Aided Mol. Design,
2001, 15, 41-55.
46.
Liu, N.; Samartzidou, H.; Lee, K. W.; Briggs, J. M.; Delcour, A. H. “Effects of
Pore Mutations and Permeant Ion Concentration on the Spontaneous Gating
Activity of OmpC Porin”, Protein Eng., 2000, 13, 491-500.
45.
Lins, R. D.; Straatsma, T. P.; Briggs, J. M. “Similarities in the HIV-1 and ASV
Integrase Active Site upon Metal Binding", Biopolymers, 2000, 53, 308-15.
44.
Soares, T. A.; Briggs, J. M.; Goodsell, D.; Olson, A. “
43.
Carlson, H. A.; Masukawa, K. M.; Rubens, K.; Bushman, F. D.; Jorgensen, W. L.;
Lins, R. D.; Briggs, J. M.; McCammon, J. A. "Developing a Dynamic
Pharmacophore Model for HIV-1 Integrase", J. Med. Chem., 2000, 43, 2100-2114.
42.
Lins, R. D.; Adesokan, A.; Soares, T. A.; Briggs, J. M. “Investigations on
Human Immunodeficiency Virus Type-1 Integrase/DNA Binding Interactions via
Molecular Dynamics and Electrostatics Calculations”, Pharm. Therap., 2000, 85, 123-131.
41.
Blachut-Okrasinska, E.; Lesyng, B.; Briggs, J. M.; McCammon, J. A.;
Antosiewicz, J. M. “Poisson-Boltzmann model studies of Molecular Electrostatic
Properties of the cAMP-Dependent Protein Kinase”, Eur. Biophys. J., 1999, 28, 457-467.
40.
Soares, T. A.; Goodsell, D. S.; Briggs, J. M.; Ferreira, R.; Olson, A. J.
“Docking of 4-Oxalocrotonate Tautomerase Substrates: Implications for the
Catalytic Mechanism”, Biopolymers, 1999, 50, 319-328.
39.
Scheeff, E. D.; Briggs, J. M.; Howell, S. B. “Molecular Modeling of the
Intrastrand Guanine-Guanine Adducts produced by Cisplatin and Oxaliplatin”, Mol. Pharm., 1999, 56, 633-643.
38. Lins, R. D.; Briggs, J. M.; Straatsma, T. P.;
Carlson, H. A.; Greenwald, J.; Choe, S.; McCammon, J. A. “Molecular Dynamics
Studies of the HIV-1 Integrase Catalytic Domain”, Biophys. J., 1999, 76, 2999-3011.
37.
Carlson, H. A.; Briggs, J. M.; McCammon, J. A. “Calculation of the Titration
Curves of the Ligands and Side Chains of E.
Coli D-ala:D-ala Ligase”, J. Med.
Chem., 1999, 42, 109-117.
36.
Briggs, J. M.; Antosiewicz, J. “Simulation of pH-dependent Properties of
Proteins Using Mesoscopic Models”, In “Reviews in Computational Chemistry”, K.
N. Lipkowitz and D. B. Boyd, Eds., 1999,
Vol. 13, Ch. 5, 249-311.
35.
Antosiewicz, J.; Blachut-Okrasinska, E.; Grycuk, T.; Briggs, J. M.; Wlodek, S.
T.; Lesyng, B.; McCammon, J. A. “Prediction of pKas of Titratable Residues in
Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System”, In
“Computational Molecular Dynamics: Challenges, Methods, Ideas”, P. Deuflhard,
J. Hermans, B. Leimkuehler, A. Mark, R. D. Skeel, S. Reich, Eds., (Lecture
Notes in Computational Science and Engineering), Springer, 1999, vol. 4, pgs. 176-196,
34.
de Bakker, P. I. W.; Tara, S.; Briggs, J. M. “Thermodynamic Correlation with
Kinetic Association Rates for Several Mutants of Mouse Acetylcholinesterase” In
“Structure and Function of Cholinesterases and Related Proteins”, B. P. Doctor,
D. M. Quinn, R. L. Rotundo, P. Taylor, Eds., Plenum Pubs., pgs., 1998.
33.
Weber, W.; Demirdjian, H.; Lins, R. D.; Briggs, J. M.; Ferreira, R.; McCammon,
J. A. “Brownian and Essential Dynamics Studies of the HIV-1 Integrase Catalytic
Domain”, J. Biomolecular Str. Dynamics,
1998, 16, 733-745.
32.
Tara, S.; Elcock, A. H.; Kirchhoff, P. D.; Briggs, J. M.; Radic, Z.; Taylor,
P.; McCammon, J. A. “Rapid Binding of a Cationic Active-Site Inhibitor to
Wild-Type and Mutant Murine Acetylcholinesterase: Brownian Dynamics
Simulation”, Biopolymers, 1998, 46, 465-474.
31.
Zhou, H.-X.; Briggs, J. M.; Tara, S.; McCammon, J. A. “Correlation between Rate
of Enzyme-Substrate Diffusional Encounter and Average Boltzmann Factor around
Active Site”, Biopolymers, 1998, 45, 355-360.
30.
Madura, J. D.; Briggs, J. M.; Wade, R. C.; Gabdoulline, R. “Brownian Dynamics”
in The Encyclopedia of Computational
Chemistry, Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.;
Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R. (Eds.); John Wiley &
Sons: Chichester, 1998, vol. 1,
141-154.
29.
Fogolari, F.; Esposito, G; Viglino, P.; Briggs, J. M.; McCammon, J. A. “pKa
Shift Effects on Backbone Amide Base-Catalyzed Hydrogen Exchange Rates in
Peptides”, J. Am. Chem. Soc., 1998, 120, 3735-3738.
28.
Fogolari, F.; Briggs, J. M. “On the Variational Approach to Poisson-Boltzmann
Free Energies”, Chem. Phys. Lett., 1997, 281, 135-139.
27.
Baginski, M.; Fogolari, F.; Briggs, J. M. “Electrostatic and Non-electrostatic
Contributions to the Binding Free Energies of Anthracycline Antibiotics to
DNA”, J. Mol. Biol., 1997, 274, 253-267.
26.
Madura, J. D.; Lombardini, J. B.; Briggs, J. M.; Minor, D. L.; Wierzbicki, A.
“Physical and Structural Properties of Taurine and Taurine Analogs”, Amino Acids, 1997, 13, 131-139.
25.
Wlodek, S.; Antosiewicz, J.; Briggs, J. M. “On the Mechanism of Action of
Acetylcholinesterase: The Electrostatically Induced Acceleration of the
Catalytic Acylation Step”, J. Am. Chem.
Soc., 1997, 119, 8159-8165.
24. Briggs, J. M. “Protein-Protein Diffusional
Encounter”, Biophys. J.,
1997, 72, 1915-1916 (New and Notable).
23.
Costante-Crassous, J.; Marrone, T. J.; Briggs, J. M.; Collet, A.; McCammon, J.
A. “Absolute Configuration of Bromochlorofluoromethane from Molecular Dynamics
Simulation of its Enantioselective Complexation with Cryptophane-C”, J. Am. Chem. Soc., 1997, 119, 3818-3123
22.
Fogolari, F.; Elcock, A. H.; Esposito, G.; Viglino, P.; Briggs, J. M.;
McCammon, J. A. “Electrostatic Effects in Homeodomain-DNA Interactions”, J. Mol. Biol., 1997, 267, 368-381.
21.
Marrone, T. J.; Briggs, J. M.; McCammon, J. A. “Structure-based Drug Design:
Computational Advances”, Ann. Rev. Pharm.
Toxicology, 1997, 37, 71-90. (invited contribution).
20.
Zhou, H.-X.; Briggs, J. M.; McCammon, J. A. “A 240-fold Electrostatic
Rate-Enhancement for Acetylcholinesterase-Substrate Binding Can Be Predicted by
the Potential within the Active Site”, J.
Am. Chem. Soc., 1996, 118, 13069-13070.
19.
Briggs, J. M.; Marrone, T. J.; McCammon, J. A. “Computational Science: New
Horizons and Relevance to Pharmaceutical Design” Trends in Cardiovascular Medicine, 1996, 6, 198-204.
(invited contribution, cover image)
18.
Antosiewicz, J.; Briggs, J. M.; Elcock, A. H.; Gilson, M. K.; McCammon, J.
A. “Computing the Ionization States of
Proteins with a Detailed Charge Model”, J.
Comp. Chem., 1996, 17, 1633-1644.
17.
Kirchhoff, P. D.; Bass, M. B.; Hanks, B. A.; Briggs, J. M.; Collet, A.;
McCammon, J. A. “Structural Fluctuations of a Cryptophane Host: A Molecular
Dynamics Simulation”, J. Am. Chem. Soc.,
1996, 118, 3237-3246.
16.
Antosiewicz, J,; Briggs, J. M.; McCammon, J. A. “Ionic Strength Dependence of
Hydrodynamic Torque Orientational Steering Effects in Enzyme-Substrate
Association”, European Biophysics Journal,
1996, 24, 137-141.
15.
Wlodek, S.; Antosiewicz, J.; Gilson, M. K.; Straatsma, T. P.; Humblet, C.;
Briggs, J. M.; Sussman, J.; McCammon, J. A. “The Binding of Tacrine and
Chlorotacrine to Acetylcholinesterase”, Biopolymers,
1996, 38, 109-117.
14.
Marrone, T. J.; Straatsma, T. P.; Briggs, J. M.; Wilson, D. K.; Quiocho, F. A.;
McCammon, J. A. “Theoretical Study of Inhibition of Adenosine Deaminase by
8R-Coformycin and 8R-Deoxycoformycin”, J.
Med. Chem., 1996, 39, 277-284.
13.
Madura, J. D.; Briggs, J. M.; Wade, R. C.; Davis, M. E.; Luty, B. A.; Ilin, A.;
Antosiewicz, J.; Gilson, M. K.; Bagheri, B.; Scott, L. R.; McCammon, J. A.
“Electrostatics and Diffusion of Molecules in Solution: Simulations with the
University of Houston Brownian Dynamics Program”, Comp. Phys. Commun., 1995,
91, 57-95 (invited contribution).
12.
Cannon, W. R.; Briggs, J. M.; Shen, J.; McCammon, J. A.; Quiocho, F. A.
“Conservative and Nonconservative Mutations in Proteins: Anomalous Mutations in
a Transport Receptor Analyzed by Free Energy and Quantum Chemical
Calculations”, Protein Science, 1995, 4, 387-393.
11.
Ilin, A.; Bagheri, B.; Scott, L. R.; Briggs, J. M.; McCammon, J. A.
“Parallelization of Poisson-Boltzmann and Brownian Dynamics Calculations” ACS Symposium Series 592: Parallel Computing
in Computational Chemistry, March
13-17, 1994, Timothy G. Mattson, Ed., American Chemical Society,
Washington, DC 1995, pages 170-185.
10.
Evanseck, J. D.; Houk, K. N.; Briggs, J.
M.; Jorgensen, W. L. “Quantification of Solvent Effects on the Acidities of Z
and E Esters from Fluid Simulations”, J.
Am. Chem. Soc., 1994, 116, 10630-10638.
9. Wade,
R. C.; Luty, B. A.; Demchuk, E.; Madura, J. D.; Davis, M. E.; Briggs, J. M.;
McCammon, J. A. “Enzyme-Substrate Encounter with Gated Active Sites”, Nature Structural Biology, 1994, 1, 65-69.
8. Luty, B. A.; Wade, R. C.; Madura, J. D.;
Davis, M. E.; Briggs, J. M.; McCammon, J. A. “Brownian Dynamics Simulations of
Diffusional Encounters between Triose Phosphate Isomerase and Glyceraldehyde
Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate”, J. Phys. Chem., 1993, 97, 233-237.
7. Briggs,
J. M.; J. A. McCammon “Computation Unravels Mysteries of Molecular Biophysics” Computers in Physics, 1992, 6, 238-243 (featured article).
6. Briggs,
J. M.; Jorgensen, W. L.; Nguyen, T. B. “Monte Carlo Simulations of Liquid
Acetic Acid and Methyl Acetate with the OPLS Potential Functions”, J. Phys. Chem., 1991, 95, 3315-3322.
5. Briggs,
J. M.; Matsui, T.; Jorgensen, W. L. “
4. Jorgensen,
W. L.; Briggs, J. M.; Contreras, M. L. “Relative Partition Coefficients for
Organic Solutes from Fluid Simulations”, J.
Phys. Chem., 1990, 94, 1683-1686.
3. Jorgensen,
W. L.; Briggs, J. M. “A Priori pKa
Calculations and the Hydration of Organic Ions”, J. Am. Chem. Soc., 1989,
111, 4190-4197.
2. Jorgensen,
W. L.; Briggs, J. M. “Monte Carlo Simulations of Liquid Acetonitrile with a
Three-Site Model”, Mol. Phys., 1988, 63, 547-558.
1. Jorgensen,
W. L.; Briggs, J. M.; Gao, J. “A Priori
Calculations of pKa's for Organic Compounds in Water: The pKa of Ethane”, J. Am. Chem. Soc., 1987, 109, 6857-6858.