SELECTED PUBLICATIONS
Research
Interests
Selected Publications
88. Forcefields for Simulations of Proteins Containing Multi/Heavy Metal Ions. Dmitri V. Sakharov and Carmay Lim*, J. Phys. Chem. B (2007), submitted.
87. Effect of Metal–Binding Site Geometry on Protein Structure, Mobility, and Function. Jon D. Wright, and Carmay Lim*, Proteins: Structure, Function, and Bioinformatics (2007), under revision
86. Mononuclear vs. Binuclear Metal-Binding Sites: Metal Binding Affinity and Selectivity from PDB Survey and DFT/CDM Calculations. Tsung-YingYang, Todor Dudev, and Carmay Lim**, J. Am. Chem. Soc. (2007), under revision.
85. The Role of Water in Metal Binding and Selectivity in Proteins. Todor Dudev and Carmay Lim*, Accounts Chem. Res. (2006).
84. Predicting DNA-Binding Sites on Proteins from Electrostatic Stabilization upon Mutation to Asp/Glu and Evolutionary Conservation. Yao Chi Chen, Chih Yuan Wu, and Carmay Lim*, Bioinformatics (2006), submitted.
83. Toward Absolute Density of States Calculation for Proteins. David Sullivan and Carmay Lim*, J. Phys. Chem. B (2006), submitted.
82. Characterizing Polypeptide Conformational Spaces: Dependence on Thermodynamical Variables and Energy Components. David Sullivan and Carmay Lim*, J. Phys. Chem. B (2006), submitted.
81. Factors Governing the Metal Coordination Number in Group IA and IIA Metal Hydrates From DFT Calculations. Ingvar Tunell and Carmay Lim*, Inorg. Chem. (2006), submitted.
80. Factors Governing the Metal Coordination Number in Metal Complexes From Cambridge Structure Database Analyses. Minko Dudev, Jonathan Wang, Todor Dudev and Carmay Lim*, J. Phys. Chem. B (2006), 110: 1889-1895.
79. Factors Governing the Maximum Number of Metal-bound Carboxylates in Metalloproteins Tudor Dudev and Carmay Lim*, J. Am. Chem. Soc. (2006) 128: 1553-1561.
78. Empirical Force Field For Biologically Active Divalent Metal Cations in Water. C. Satheesan Babu and Carmay Lim*, J. Phys. Chem. B (2006) 110: 691-699.
77. Insights into Mercury Poisoning Mechanisms from Computational Studies of the Coordination Stereochemistry, Bonding, and Metal Selectivity of Mercury. Hui-Chung Tai and Carmay Lim*. J. Phys. Chem. A (2006) 110: 452-462.
76. Differential Effects of the Zn-His-[Asp/Glu,Bkb] Triad on Zn-core Stability and Reactivity. Yen-lin
Lin, Yu-ming Lee, and Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 11336-11347.
75. Zn Protein Simulations Including Charge Transfer and Local Polarization Effects. Dmitri V.
Sakharov and Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 4923-4931.
74. Factors Governing the Substitution of La3+ for Ca2+ and Mg2+in Metalloproteins: A DFT/CDM
Study. Todor Dudev, Li-Ying Chang, and Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 4091-
4103.
73. Configurational Entropy of Proteins: Covariance Matrix vs. Cumulative Distribution Calculations. David Sullivan and Carmay Lim*, J. Chin. Chem. Soc. (2004) 51: 1209-1219.
72. Oxyanion Selectivity in Sulfate and Molybdate Transport Proteins: An Ab Initio/CDM Study. Todor
Dudev and Carmay Lim*, J. Am. Chem. Soc. (2004) 126: 10296-10305.
71. Bidentate vs. Monodentate Carboxylate Binding in Magnesium and Calcium Proteins: What Are the
Basic Principles? Todor Dudev and Carmay Lim*, J. Phys. Chem. B (2004) 108: 4546-4557.
70. Factors Governing the Protonation State of Zn-bound Histidine in Proteins. Yen-lin Lin and Carmay Lim*, J. Am. Chem. Soc. (2004) 126: 2602-2612.
69. A Combined Experimental and Theoretical Study of Divalent Metal Ion Selectivity and Function in Proteins. Application to E. coli Ribonuclease H1. C. Satheesan Babu, Todor Dudev, Ruby Casareno, Jimmy A. Cowan, and Carmay Lim*, J. Am. Chem. Soc. (2003) 125: 9318-9328.
68. First–Second Shell Interactions in Metal Binding Sites in Proteins: A PDB Survey and DFT/CDM Calculations. Todor Dudev, Yen-lin Lin, Minko Dudev, and Carmay Lim*, J. Am. Chem. Soc. (2003) 125: 3168-3180.
67. Metal Binding and Selectivity in Zinc Proteins. Todor Dudev* and Carmay Lim*, J. Chin. Chem. Soc. (2003) 50: 1093-1102.
66. Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins. Todor Dudev* and Carmay Lim*, Chemical Reviews (2003) 103: 773-787.
65. Inducing Antigenic Cross-reactivity against B cells in Mice by Immunizing with Human Iga to Mice. Jim J.C. Sheu, Tammy Cheng, Carmay Lim, and Tse Wen Chang*, J. Immunology (2003) 170: 1158-1166.
64. Nonconvergence of the Solute Potential in an Infinite Solvent and Its Implications in Continuum Models. Pei-Kun Yang and Carmay Lim*, J. Phys. Chem. B (2002) 106: 12093-12096.
63. On the Charge and Molecule Based Summations of Solvent Electrostatic Potentials and the Validity of Electrostatic Linear Response in Water. C. Satheesan Babu, Pei-Kun Yang and Carmay Lim*, J. Biol. Phys. (2002) 28: 95-113.
62. Representing an Infinite Solvent System with a Rectangular Finite System Using Image Charges.
Pei-Kun Yang, Shu-Huey Liaw and Carmay Lim*, J. Phys. Chem. B (2002) 106: 2973-2982.
61. Factors Governing Intrinsic Chemical Reactivity Differences between Clavulanic and Penicillanic Acids. Yen-lin Lin, Nai-yuan Chang and Carmay Lim*, J. Am. Chem. Soc. (2002) 124: 12042-12053.
60. Long-Range Effects of Mutating R248 to Q/W in the p53 Core Domain. Sergey Yu Noskov, Jon D. Wright, and Carmay Lim*, J. Phys. Chem. B (2002) 106: 13047-13057.
59. Factors Governing Loss & Rescue of DNA Binding upon Single & Double Mutations in the p53-CD. Jon D. Wright, Sergey Yu Noskov and Carmay Lim*, Nucleic Acids Research (2002) 30: 1563-1574.
58. Factors Governing the Protonation State of Cysteines in Proteins. An Ab Initio/CDM Study. Todor Dudev and Carmay Lim*, J. Am. Chem. Soc. (2002) 124: 6759-6766.
57. Constructing a Human Membrane and Secreted Protein-enriched cDNA Library using a Minimal Set of PCR Primers. Fan Yi, Chih Yuan Wu, Cheng Wei Chen, Tse Wen Chang* and Carmay Lim*, Nucleic Acids Research (2001) 29: e114.
56. Free Energy Decomposition of Protein-Protein Interactions. Sergey Yu Noskov and Carmay Lim*, Biophys. J. (2001) 81: 737-750.
55. A Fast Method For Predicting Amino Acid Mutations That Lead to Unfolding. Jon D. Wright and Carmay Lim*, Prot. Engineering (2001) 14: 479-486.
54. Incorporating Nonlinear Solvent Response in Continuum Dielectric Models Using A Two-Sphere Description of the Born Radius. C. Satheesan Babu and Carmay Lim*, J. Phys. Chem. A (2001) 105: 5030-5036.
53. Solvation Free Energies of Polar Molecular Solutes: Application of the Two-sphere Born Radius in Continuum Models of Solvation. C. Satheesan Babu and Carmay Lim*, J. Chem. Phys. (2001) 114: 889-899.
52. Modeling Zn2+-Cysteinate Complexes in Proteins. Todor Dudev and Carmay Lim*, J. Phys. Chem. B (2001) 105: 10709-10714.
51. Metal Selectivity in Metalloproteins: Zn2+ vs. Mg2+. Todor Dudev and Carmay Lim*, J. Phys. Chem. B (2001) 105: 4446-4452.
50. Conformational Analysis of Long Spacers in PROSITE Patterns. Kuen-Yi Lin, Jon Wright and Carmay Lim*, J. Mol. Biol. (2000) 299: 537-548.
49. Design, Synthesis, and SAR of Novel Carbapenem Antibiotics with High Stability to Xanthomonas maltophilia Oxyiminocephalosporinase Type II. Gholam H. Hakimelahi*, Ali A. Moosavi-Mohavedi, Shwu-Chen Tsay, Fu-Yuan Tsai, Jon Wright, Todor Dudev, Shahram Hakimelahi, and Carmay Lim*, J. Med. Chem. (2000) 43: 3632-3640.
48. Tetrahedral vs. Octahedral Zinc Complexes with Ligands of Biological Interest: A DFT/CDM Study. Todor Dudev and Carmay Lim*, J. Am. Chem. Soc. (2000) 122: 11146-11153.
47. Metal Binding in Proteins: The Effect of the Dielectric Medium. Todor Dudev and Carmay Lim*, J. Phys. Chem. B (2000) 104: 3692-3694.
46. Theory of Ionic Hydration: New Insights from Simulation and Experiment. C. Satheesan Babu and Carmay Lim*, J. Phys. Chem. B (1999) 103: 7958-7968.
45. A New Interpretation of the Effective Born Radius from Simulation and Experiment. C. Satheesan Babu and Carmay Lim*, Chem. Phys. Lett. (1999) 310: 225-228.
44. Incremental Binding Free Energies In Mg2+ Complexes: A DFT Study. Todor Dudev and Carmay Lim*, J. Phys. Chem. A (1999) 103: 8093-8100.
43. Competitive Binding in Mg Coordination Chemistry: Water vs Ligands of Biological Interest. Todor Dudev, Jimmy Cowan and Carmay Lim*, J. Am. Chem. Soc. (1999) 121: 7665-7673.
42. Ring Strain vs. Solvent Effects in Phosphate Base Hydrolysis. Carmay Lim, Phosphorus, Sulfur and Silicon (1999) 144-146: 769-773.
41. Exploring the Dynamic Information Content of a Protein NMR Structure: Comparison of a Molecular Dynamics Simulation with the NMR and X-Ray Structures of E. Coli RNase HI. Marios Philippopoulos and Carmay Lim*, Proteins: Structure, Function and Genetics (1999) 36: 87-110.
40. Prediction of an Anti-IgE Binding Site on IgE. Jon Wright and Carmay Lim*, Protein Engineering (1998) 11: 421-427.
39. Ring Strain Energies from Ab Initio Calculations. Todor Dudev and Carmay Lim*, J. Am. Chem. Soc. (1998) 120, 4450-4458.
38. Factors Governing the Enhanced Reactivity of Five-Membered Cyclic Phosphate Esters. Nai-Yuan Chang and Carmay Lim*, J. Am. Chem. Soc. (1998) 120, 2156-2167.
37. Protein Dynamics: Molecular Dynamics Simulation, NMR Spectroscopy and X-ray Crystallography. Marios Philippopoulos and Carmay Lim*, in Advances in Computational Life Sciences Vol. 2: Humans to Proteins. M. Michalewicz (Editor), CSIRO Mathematical and Information Sciences (1998).
36. An ab Initio Study of Nucleophilic Attack of Trimethyl Phosphate. Nai-Yuan Chang and Carmay Lim*, J. Phys. Chem. A (1997) 101, 8706-8713.
35. Accuracy and Precision of NMR Relaxation Experiments and MD Simulations for Characterizing Protein Dynamics. Marios Philippopoulos, Arthur Mandel, Arthur G. Palmer III* and Carmay Lim*, Proteins: Structure, Function, and Genetics (1997) 28, 481-493.
34. The Binding Mode of an E-64 Analog to the Active site of Cathepsin B. Ming Hsiang Feng, Shek Ling Chan, YueFang Xiang, Carol P. Huber and Carmay Lim*, Protein Engineering (1996) 9, 977-986.
33. Structural Characterization of the Phosphotyrosine Binding Region of a High Affinity SH2 Domain-Phosphopeptide Complex by MD Simulation and Chemical Shift Calculations. Ming-Hsiang Feng, Marios Philippopoulos, Alexander D. MacKerell Jr. and Carmay Lim*, J. Am. Chem. Soc. (1996) 118, 11265-11277.
32. Positive Charge at Position 549 is Essential for Phosphatidylinositol 4,5-Bisphosphate- but not Phosphatidylinositol-Hydrolyzing Activities of Human Phospholipase Cδ1. Li-Ping Wang, Carmay Lim, Y.-S. Kuan, Chih-lin Chen, Hwei-Fang Chen and King Klim*, J. Biol. Chem. (1996) 271, 24505-24516.
31. A Commentary on the Relationship Between Continuum Dielectric Theory, and Thermodynamics. Shek Ling Chan, Wen Ching Hu and Carmay Lim*, Proceedings of HPC-Asia (1995).
30. Dynamic Model of Lignin Growing in Restricted Spaces. Marc Roussel and Carmay Lim*, Macromolecules (1995) 28, 370-376.
29. Discrete, Dynamic Polymer Modeling: A Pseudo-Diatomic Model of Lignin. Marc Roussel and Carmay Lim*, J. Comp. Chem. (1995) 16, 1181-1191.
28. Identifying the Mechanism of Protein Loop Closure: A Molecular Dynamics Simulation of the Bacillus Stearothermophilus LDH Loop in Solution. Marios Philippopoulos, YueFang Xiang, and Carmay Lim*, Protein Engineering (1995) 8, 565-573.
27. Molecular Dynamics Simulation of E. Coli Ribonuclease HI in Solution: Correlation with NMR and X-ray Data and Insights into Biological Function. Marios Philippopoulos and Carmay Lim*, J. Mol. Biol. (1995) 254, 771-792.
26. Solution Free Energies from a Combined Quantum Mechanical & Continuum Dielectric Approach. Carmay Lim*, Shek Ling Chan, and Philip Tole, in ACS Symposium Series No. 568: Structure and Reactivity in Aqueous Solution. C.J. Cramer and G.D. Truhlar (editors), American Chemical Society (1994).
25. Computational Approaches to the Blood Substitute Problem. Shek Ling Chan and Carmay Lim*, Chemistry (1994) 52, 261-268.
24. Conformational Distribution of a Tetrapeptide in Solution Using a Combined Random Search and Continuum Dielectric Approach. Shek Ling Chan and Carmay Lim*, J. Phys. Chem. (1994) 98, 12805-12814.
23. Internal Motions in the Molecular Tumbling Regime: Effect on NMR Dipolar Cross-relaxation and Interproton Distance Determination. Marios Philippopoulos and Carmay Lim*, J. Phys. Chem. (1994) 98, 8264-8273.
22. Reducing the Error due to the Uncertainty in the Born Radius in Continuum Dielectric Calculations. Shek Ling Chan and Carmay Lim*, J. Phys. Chem. (1994) 98, 692-695.
21. The Double Catalytic Triad, Cys25-His159-Asp158 and Cys25-His159-Asn175, in Papain Catalysis: Role of Asp158 and Asn175. Jing Wang, YueFang Xiang, and Carmay Lim*, Protein Engineering (1994) 7, 75-82.
20. The Significance of Electrostatic Effects in Phospho-Ester Hydrolysis. Philip Tole and Carmay Lim*, J. Am. Chem. Soc. (1994) 116, 3922-3931.
19. Simulation Analysis of the Binding Interactions in the RNase A/3’-UMP Enzyme-Product Complex as a Function of pH. John Straub, Carmay Lim and Martin Karplus*, J. Am. Chem. Soc. (1994) 116, 2591-2599.
18. Do Stereoelectronic Effects Control the Structure and Reactivity of TBP Phospho-esters?. Philip Tole and Carmay Lim*, in ACS Symposium Series No. 539: The Anomeric Effect and Associated Stereoelectronic Effects. G.R. Thatcher (ed.), Am. Chem. Soc. (1993).
17. New Insights into the Base-Catalyzed Hydrolysis of Methyl Ethylene Phosphate. Philip Tole and Carmay Lim*, J. Phys. Chem. (1993) 97, 6212-6219.
16. Concerted Hydroxyl Ion Attack and Pseudorotation in a Quantum Mechanical Study of Methyl Ethylene Phosphate Hydrolysis. Carmay Lim* and Philip Tole, J. Phys. Chem. (1992) 96, 5217-5218.
15. Endocyclic and Exocyclic Cleavage of Phosphorane Monoanion: A Detailed Mechanism of the RNase A Transphosphorylation Step. Carmay Lim* and Philip Tole, J. Am. Chem. Soc. (1992) 114, 7245-7252.
14. Absolute pKa Calculations with Continuum Dielectric Methods. Carmay Lim, Don Bashford, and Martin Karplus*, J. Phys. Chem. (1991) 95, 5610-5620.
13. Dianionic Pentacoordinate Species in the Base-Catalyzed Hydrolysis of Ethylene and Dimethyl Phosphate. Annick Dejaegere, Carmay Lim and Martin Karplus*, J. Am. Chem. Soc. (1991) 113, 4353-4355
12. Nonexistence of Dianionic Pentacovalent Intermediates in an ab Initio Study of the Base-Catalyzed Hydrolysis of Ethylene Phosphate. Carmay Lim and Martin Karplus*, J. Am. Chem. Soc. (1990) 112, 5872-5873.
11. Simulation Analysis of Structures on the Reaction Pathway of RNase A. Karen Haydock, Carmay
Lim, Axel Brünger, and Martin Karplus*, J. Am. Chem. Soc. (1990) 112, 3826-3831.
10. Molecular and Harmonic Dynamics Simulations of Proteins. Carmay Lim, Dzung Nguyen, John
Straub, Bruce Tidor, and Martin Karplus, John von Neumann National Supercomputer Center,
Annual Research Report (1988).
9. Trajectory Studies of Hyperthermal Xenon Scattering from GaAs (110). Carmay Lim, John C.
Tully, Aviv Amirav, Paula Trevor, and Mark J. Cardillo, J. Chem. Phys. (1987) 87, 1808-1816.
8. Atom-surface Scattering Dynamics at Hyperthermal Energies. Aviv Amirav, Mark J. Cardillo, Paula Trevor, Carmay Lim and John C. Tully, J. Chem. Phys. (1987) 87, 1796-1807.
7. Molecular Dynamics of Nonequilibrium Infrequent Events: Laser-induced Desorption from Surfaces. Carmay Lim and John C. Tully, J. Chem. Phys. (1986) 85, 7423-7433.
6. The Effect of Vibrational-Rotational Disequilibrium on the Rate Constant for an Atom-Transfer Reaction. Carmay Lim and Donald G. Truhlar*, J. Phys. Chem. (1986) 90, 2616-2634.
5. New Techniques for the Study of Nonequilibrium Effects in Non-First-Order Systems. Carmay Lim and Donald G. Truhlar, Chem. Phys. Lett. (1985) 114, 253-257.
4. Internal-state Nonequilibrium Effects for a Fast, Second-Order Reaction. Carmay Lim and Donald G. Truhlar*, J. Phys. Chem. (1985) 89, 5-7.
3. Study of Mixture Effects in the Nonequilibrium Kinetics of Homonuclear Diatomic Dissociation and Recombination. Carmay Lim and Donald G. Truhlar*, J. Phys. Chem. (1984) 88, 778-792.
2. Nonequilibrium Effects in Chemical Kinetics: Straight-Line Paths for Homo-nuclear Diatomic Dissociation-Recombination Process. Carmay Lim and Donald G. Truhlar*, J. Phys. Chem. (1983) 81, 2683-2699.
1. The Existence of Straight-Line Paths, Invariant Vectors, and Invariant Tensors Characterizing Nonequilibrium State Distributions during Chemical Reactions. Carmay Lim and Donald G. Truhlar, J. Chem. Phys. (1983) 79, 3296-3306.