Academia Sinica Life Science Library -- Publications

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Publications

Inst. of Biomedical Sciences - 林小喬 LIM, CARMAY

Journal

Karen Sargsyan*, Karine Mazmanian*, (Carmay Lim)*. A 2023: to small molecule drugs and application to SARS-CoV-2. SCIENTIFIC REPORTS. 13, 502, 2023. [JCR]　[WOS]
Sahana Shankar, Zi-Ting Hsu, Artur Ezquerra, Chien-Chien Li, Tzu-Lun Huang, Etienne Coyaud, Cédric Grauffel, Brian Raught, Carmay Lim, Jens Lüders*, Su-Yi Tsai*, and Kuo-Chiang Hsia*. A g-tubulin complex-dependent pathway suppresses unscheduled ciliogenensis by promoting cilia disassembly. Cell Reports. 41, 111642, 2022-11-15. [JCR]　[WOS]
Cédric Grauffel*, Wei-Hsiang Weng, (Carmay Lim*). Factors Allowing Small Monovalent Li+ to Displace Ca2+ in Proteins. Phys. Chem. Chem. Phys.. 24, 17759, 2022-07-05. [JCR]　[WOS]
Wen-Hao Tsai (蔡文豪), Cédric Grauffel, Ming-Yueh Huang (黃名鉞), Sandra Postić, Marjan Slak Rupnik, Carmay Lim (林小喬), Shi-Bing Yang (楊世斌)*. Allosteric coupling between TM4 and selectivity filter regulates extracellular pH gating of TALK1 potassium channels. J. Biol.Chem.. 298, 101998, 2022-04-29. [JCR]　[WOS]
Ting Chen, Cédric Grauffel, Wei-Zen Yang, Yi-Ping Chen, Hanna S. Yuan* and (Carmay Lim*). Efficient strategy to design protease inhibitors: Application to enterovirus 71 2A protease. ACS Bio & Med Chem Au. 4, 437-449, 2022-04-19. [JCR]　[WOS]
Karine Mazmanian, Ting Chen, Karen Sargsyan, & Carmay Lim*. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WIRES Computational Molecular Science. 12, e1607, 2022-02-13. [JCR]　[WOS]
Yao Chi Chen*, Yu-Hsien Chen, Jon D. Wright, and (Carmay Lim*). PPI-HotspotDB: Database of Protein!Protein Interaction Hot Spots. J. Chem. Inf. Model.. 62, 1052-1060, 2022-02-11. [JCR]　[WOS]
Todor Dudev,* Cedric Grauffel,* and (Carmay Lim*). Calcium in signaling: Its specificity and vulnerabilities towards biogenic and abiogenic metal ions. The Journal of Physical Chemistry B. 125,37, 10419-10431, 2021-09. [JCR]　[WOS]
Cédric Grauffel*, Wei-Hsiang Weng, Todor Dudev,(Carmay Lim*). The trinuclear calcium site in the C2 domain of PKCα/γis prone to lithium attack. ACS Omega. 6,31, 20657-20666, 2021-07. [JCR]　[WOS]
Babu C. Satheesan, Lim Carmay. Influence of solution ionic strength on the stabilities of M20 loop conformations in apo E. coli dihydrofolate reductase. The Journal of Chemical Physics. 154(19), 195103, 2021-05. [JCR]　[WOS]
Grauffel Cédric, Dudev Todor, Lim Carmay. Metal Affinity/Selectivity of Monophosphate-Containing Signaling/Lipid Molecules. Journal of Chemical Theory and Computation. 17(4), 2444-2456, 2021-04. [JCR]　[WOS]
Chen Ting, Fei Cheng-Yin, Chen Yi-Ping, Sargsyan Karen, Chang Chun-Ping, Yuan Hanna S., Lim Carmay. Synergistic Inhibition of SARS-CoV-2 Replication Using Disulfiram/Ebselen and Remdesivir. ACS Pharmacology & Translational Science. 4(2), 898-907, 2021-03. [JCR]　[WOS]
He Mei-Ying, Lin Yu-Jen, Kao Yi-Ling, Kuo Pu, Grauffel Cédric, Lim Carmay, Cheng Yi-Sheng, Chou Hsin-Hung David. Sensitive and Specific Cadmium Biosensor Developed by Reconfiguring Metal Transport and Leveraging Natural Gene Repositories. ACS Sensors. 6(3), 995-1002, 2021-01. [JCR]　[WOS]
Amin Kazi S., Hu Xiaojuan, Salahub Dennis R., Baldauf Carsten, (Lim Carmay)*, Noskov Sergei*. Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset. The Journal of Chemical Physics. 153(14), 144102, 2020-10. [JCR]　[WOS]
Sargsyan Karen, Lin Chien-Chu, Chen Ting, Grauffel Cédric, Chen Yi-Ping, Yang Wei-Zen, Yuan Hanna S*., (Lim Carmay)*. Multi-targeting of functional cysteines in multiple conserved SARS-CoV-2 domains by clinically safe Zn-ejectors. Chemical Science. 11(36), 9904-9909, 2020-08. [JCR]　[WOS]
Sousa Sérgio F., Calixto Ana R., Ferreira Pedro, Ramos Maria J., (Lim Carmay)*, Fernandes Pedro A*. Activation Free Energy, Substrate Binding Free Energy, and Enzyme Efficiency Fall in a Very Narrow Range of Values for Most Enzymes. ACS Catalysis. 10(15), 8444-8453, 2020-07. [JCR]　[WOS]
Karine Mazmanian*, Karen Sargsyan, (Carmay Lim)*. How the local environment of functional sites regulates protein function. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 42, 22,, 9861-9871, 2020-05. [JCR]　[WOS]
Babu C. Satheesan*, (Lim Carmay)*. Sensitivity of Functional Loop Conformations on Long-Range Electrostatics: Implications for M20 Loop Dynamics in E. coli Dihydrofolate Reductase. Journal of Chemical Theory and Computation. 16(4), 2028-2033, 2020-03. [JCR]　[WOS]
Tai Hui-Chung, Lim Carmay. Gene Silencing Mechanisms Revealed by Dynamics of Guide, Target and Duplex Binding to Argonaute. Journal of Chemical Theory and Computation. 16(1),688-699, 2020-01. [JCR]　[WOS]
Grauffel Cédric, Dudev Todor, Lim Carmay. Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2+. Journal of Chemical Theory and Computation. 15(12),6992-7003, 2019-12. [JCR]　[WOS]
Dudev Todor, Mazmanian Karine, Weng Wei-Hsiang, Grauffel Cédric, Lim Carmay. Free and Bound Therapeutic Lithium in Brain Signaling. Accounts of Chemical Research. 52(10), 2960-2970, 2019-10. [JCR]　[WOS]
Lee YM, Grauffel C, Chen T, Sargsyan K, Lim C. Factors Governing the Different Functions of Zn(2+)-Sites with Identical Ligands in Proteins. Journal of chemical information and modeling. 59(9), 3946-3954, 2019-09. [JCR]　[WOS]
Chang CC, Chen CJ, Grauffel C, Pien YC, Lim C, Tsai SY, Hsia KC. Ran pathway-independent regulation of mitotic Golgi disassembly by Importin-alpha. Nature communications. 10(1), 4307, 2019-09. [JCR]　[WOS]
Wright Jon D., An Sung-Wan, Xie Jian, Lim Carmay, Huang Chou-Long. Soluble klotho regulates TRPC6 calcium signaling via lipid rafts, independent of the FGFR-FGF23 pathway. The FASEB Journal. 33(8),9182-9193, 2019-08. [JCR]　[WOS]
Dudev Todor, Grauffel Cédric, Hsu Shang-Te Danny, Lim Carmay. How Native and Non-Native Cations Bind and Modulate the Properties of GTP/ATP. Journal of Chemical Theory and Computation. 14(6), 3311-3320, 2018-06. [JCR]　[WOS]
Grauffel Cédric, Chu Benjamin, Lim Carmay. An efficient protocol for computing the pKa of Zn-bound water. Physical Chemistry Chemical Physics. 20(47), 29637-29647, 2018. [JCR]　[WOS]
Dudev Todor, Mazmanian Karine, Lim Carmay. Competition between Li+ and Na+ in sodium transporters and receptors: Which Na+-Binding sites are “therapeutic” Li+ targets?. Chemical Science. 9(17), 4093-4103, 2018. [JCR]　[WOS]
Grauffel Cédric, Lim Carmay. Factors governing when a metal-bound water is deprotonated in proteins. Physical Chemistry Chemical Physics. 20(47), 29625-29636, 2018. [JCR]　[WOS]
Mazmanian Karine, Dudev Todor, Lim Carmay. How First Shell–Second Shell Interactions and Metal Substitution Modulate Protein Function. Inorganic Chemistry. 57(22), 14052-14061, 2018. [JCR]　[WOS]
Dudev Todor, Grauffel Cédric, Lim Carmay. How Pb2+ Binds and Modulates Properties of Ca2+-Signaling Proteins. Inorganic Chemistry. 57(23), 14798-14809, 2018. [JCR]　[WOS]
Nuñez Nicole N., Khuu Cindy, Babu C. Satheesan, Bertolani Steve J., Rajavel Anisha N., Spear Jensen E., Armas Jeremy A., Wright Jon D., Siegel Justin B., Lim Carmay, David Sheila S. The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair. Journal of the American Chemical Society. 140(41), 13260-13271, 2018. [JCR]　[WOS]
Karen Sargsyan*, Cédric Grauffel, & Carmay Lim*. How Molecular Size Impacts RMSD Applications in Molecular Dynamics Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 13(4), 518-1524, 2017-04. [JCR]　[WOS]
Todor Dudev*, Cédric Grauffel, & Carmay Lim*. How Native and Alien Metal Cations Bind ATP. Implications for Lithium as a Therapeutic Agent. SCIENTIFIC REPORTS. 7, 42377, 2017-02. [JCR]　[WOS]
Wright Jon D., An Sung-Wan, Xie Jian, Yoon Joonho, Nischan Nicole, Kohler Jennifer J., Oliver Noelynn, Lim Carmay, Huang Chou-Long. Modeled structural basis for the recognition of α2-3-sialyllactose by soluble Klotho. The FASEB Journal. 31(8), 3574-3586, 2017. [JCR]　[WOS]
Aravind Chandrasekaran, Justin Chan, Carmay Lim,* & Lee-Wei Yang*. Protein dynamics and contact topology reveal protein-DNA binding orientation. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 12(11), 5269–5277, 2016-10. [JCR]　[WOS]
Todor Dudev*, Cédric Grauffel, & Carmay Lim*. Influence of the Selectivity Filter Properties on Proton Selectivity in the Influenza A M2 Channel. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138(39),13038–13047, 2016-09. [JCR]　[WOS]
Karine Mazmanian, Karen Sargsyan, Cédric Grauffel, Todor Dudev, & Carmay Lim*. Preferred hydrogen-bonding partners of cysteine. Implications for Regulating Cys Functions. The Journal of Physical Chemistry B. 120(39),10288–10296, 2016-09. [JCR]　[WOS]
Todor Dudev*, Karine Mazmanian, & Carmay Lim*. Factors Controlling the Na+/Mg2+ Selectivity in Sodium Transporters and Enzymes. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. 18(25), 16986-16997, 2016-07. [JCR]　[WOS]
Shih-Chieh Su, Chien-Chu Lin, Hui-Chung Tai, Mu-Yueh Chang, Meng-Ru Ho, C. Satheesan Babu, Jiahn-Haur Liao, Shih-Hsiung Wu, Yuan-Chih Chang, Carmay Lim & Chung-I Chang*. Structural basis for the magnesium-dependent activation and hexamerization of the Lon AAA+ protease. STRUCTURE. 24(5), 676–686, 2016-05. [JCR]　[WOS]
Satheesan Babu* & Carmay Lim*. Efficient Binding of Flexible and Redox-active Coenzymes by Oxidoreductases. ACS Catalysis. 6(6),3469–3472, 2016-04. [JCR]　[WOS]
Cédric Grauffel*, Carmay Lim*. Factors governing the bridging water protonation state in polynuclear Mg2+ proteins. The Journal of Physical Chemistry B. 120,1759–1770, 2016-03. [JCR]　[WOS]
Yu-Ming Lee, Yulander Duh, Shih-Ting Wang, Michael M.C. Lai*, Hanna S. Yuan* & Carmay Lim*. Using an old drug to target a new drug site: Application of disulfiram to target the Zn-site in HCV NS5A protein. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138(11), 3856–3862, 2016-03. [JCR]　[WOS]
Chien-Hao Chiang, Cédric Grauffel, Pan-Hsien Kuo, Lyudmila Doudeva, Carmay Lim, Hanna S Yuan*. Structural analysis of disease-linked TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein aggregation. Scientific Reports. 6, 21581, 2016-02. [JCR]　[WOS]
Carmay Lim, Todor Dudev. Potassium versus sodium selectivity in monovalent ion channel selectivity filters. . Metal ions in life sciences. 16, 325-47, 2016-01. [JCR]　[WOS]
Sargsyan Karen, Hua Yun Hao, (Lim, Carmay)AUG 2015. Clustangles: An Open Library for Clustering Angular Data. JOURNAL OF CHEMICAL INFORMATION AND MODELING. 55(8), 1517-1520, 2015-08. [JCR]　[WOS]
Sérgio F. Sousa, Maria J. Ramos, Carmay Lim* & Pedro A. Fernandes*. Relationship between enzyme/substrate properties and enzyme efficiency in hydrolases. ACS Catalysis. 5(10),5877–5887, 2015-08. [JCR]　[WOS]
Wright JD, Chu HM, Huang CH, Ma C, Wen Chang T, Lim C. Structural and Physical Basis for Anti-IgE Therapy. Scientific reports. 5, 11581, 2015-06. [JCR]　[WOS]
Todor Dudev, Boris Musset, Deri Morgan, Vladimir V. Cherny, Susan M.E. Smith, KArine Mazmanian, Thomas E. DeCoursey* & Carmay Lim*. Selectivity mechanism of the voltage-gated in proton channel, Hv1. Scientific Reports. 5, 10320, 2015-05. [JCR]　[WOS]
Todor Dudev, Mike Devereux, Markus Meuwly, Carmay Lim, Jean-Philip Piquemal & Nohad Gresh*. Quantum-chemistry based calibration of the alkali metal cation series (Li+– Cs+) for large-scale polarizable molecular mechanics/dynamics simulations. JOURNAL OF COMPUTATIONAL CHEMISTRY. 36(5), 285-302, 2015-02. [JCR]　[WOS]
Todor Dudev* & Carmay Lim*. Ion Selectivity in the Selectivity Filters of Acid-Sensing Ion Channels. Scientific Reports. 5, 7864, 2015-01. [JCR]　[WOS]
Todor Dudev* & Carmay Lim*. Ion Selectivity Strategies of Sodium Channel Selectivity Filters. ACCOUNTS OF CHEMICAL RESEARCH. 47(12), 3580-3587, 2015-01. [JCR]　[WOS]
Tammy M. K. Cheng*, Sebastian Heeger, Raphaël A. G. Chaleil, Nik Matthews, Aengus Stewart, Jon Wright, Carmay Lim, Paul A. Bates* & Frank Uhlmann*. A simple biophysical model emulates budding yeast chromosome condensation. eLife. 4, e05565, 2015. [JCR]　[WOS]
C. Satheesan Babu, Yu-Ming Lee, Todor Dudev & Carmay Lim*. Modeling Zn2+ Release from Metallothionein. The Journal of Physical Chemistry A. 118(39), 9244-9252, 2014-10. [JCR]　[WOS]
Yun-Hao Hua, Chih Yuan Wu, Karen Sargsyan, & Carmay Lim*. Sequence-motif detection of NAD(P)-binding proteins: Discovery of a Unique Antibacterial Drug Target. Scientific Reports. 4, 6471, 2014-09. [JCR]　[WOS]
Jiun-Jie Shie, Ying-Chih Liu, Yu-Ming Lee, Carmay Lim, Jim-Min Fang, and Chi-Huey Wong*. An Azido-BODIPY Probe for Glycosylation: Initiation of Strong Fluorescence Upon Triazole Formation. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 136(28), 9953-9961, 2014-07. [JCR]　[WOS]
Dudev T, Lim C. Evolution of eukaryotic ion channels: principles underlying the conversion of Ca(2)(+)-selective to Na(+)-selective channels. Journal of the American Chemical Society. 136(9), 3553-3559, 2014-02. [JCR]　[WOS]
Hsing-Mao Chu, Jon Wright, Yueh-Hsuan Chan, Chien-Jen Lin, Tse Wen Chang* and Carmay Lim*. Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations. Nature Communications. 5, 3139, 2014-01. [JCR]　[WOS]
Yu-Ming Lee, Yeh-Fon Lin & Carmay Lim*. Factors Controlling the Role of Zn and Reactivity of Zn-bound Cysteines in Proteins: Application to Drug Target Discovery. . Journal of the Chinese Chemical Society. 61(1), 142-150, 2014. [JCR]　[WOS]
Yao Chi Chen, Karen Sargsyan, Jon D. Wright, Yi-Shuian Huang* and Carmay Lim*. Identifying RNA-binding residues based on evolutionary conserved structural and energetic features. NUCLEIC ACIDS RESEARCH. 42(3), e15, 2013-12. [JCR]　[WOS]
Todor Dudev* and (Carmay Lim*). Importance of Metal Hydration on the Selectivity of Mg2+ versus Ca2+ in Magnesium Ion Channels. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 135(45), 17200-17208, 2013-10. [JCR]　[WOS]
Todor Dudev* and (Carmay Lim*). Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins. CHEMICAL REVIEWS. 114(1), 538-556, 2013-09. [JCR]　[WOS]
Yu-Ming Lee, Yi-Ting Wang, Yulander Duh, Hanna S. Yuan* and (Carmay Lim*). Identification of Labile Zn Sites in Drug-Target Proteins. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 135(38), 14028-14031, 2013-09. [JCR]　[WOS]
Jon Wright, Karen Sargsyan, Xiong-wu Wu, Bernie Brooks, and (Carmay Lim*). Protein−Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 9(9), 4186-4194, 2013-08. [JCR]　[WOS]
C. Satheesan Babu*, Todor Dudev and (Carmay Lim*). Differential Role of the Protein Matrix on the Binding of a Catalytic Aspartate to Mg2+ vs Ca2+: Application to Ribonuclease H . JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 135(17), 6541-6548, 2013-04. [JCR]　[WOS]
Todor Dudev* and (Carmay Lim*). Competition Among Ca2+, Mg2+, and Na+ for Ion Channel Selectivity Filters: Determinants of Ion Selectivity. JOURNAL OF PHYSICAL CHEMISTRY B. 116(35), 10703-10714, 2012-09. [JCR]　[WOS]
Yao Chi Chen, Jon Wright, (Carmay Lim*). DR_bind: a web server for predicting DNA-binding sites from the protein structure based on electrostatics, evolution and geometry. NUCLEIC ACIDS RESEARCH. 40(W1), W249-W256, 2012-07. [JCR]　[WOS]
Chih Yuan Wu, Yun-Hao Hua, Yao Chi Chen & (Carmay Lim*). Hidden Relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding Proteins. JOURNAL OF PHYSICAL CHEMISTRY B. 116 (19), 5644–5652, 2012-04. [JCR]　[WOS]
Wu PC, Chen JB, Kawamura S, Roos C, Merker S, Shih CC, Hsu BD, (Lim C), Chang TW*. The IgE gene in primates exhibits extraordinary evolutionary diversity. Immunogenetics. 64(4), 279-287, 2012-04. [JCR]　[WOS]
Todor Dudev* , (Carmay Lim*). Why voltage-gated Ca2+ and bacterial Na+ channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. 14(36), 12451-12456, 2012-03. [JCR]　[WOS]
Todor Dudev*, (Carmay Lim*). The effect of metal binding on the characteristic infrared band intensities of ligands of biological interest. J. Mol. Struct.. 1009(S1), 83-88, 2012-02. [JCR]　[WOS]
Sargsyan K, Wright J, (Lim C*). GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics. Nucleic acids research. 40, e25, 2011-12. [JCR]　[WOS]
Dudev T, (Lim C*). Competition between Li+ and Mg2+ in metalloproteins. Implications for lithium therapy. Journal of the American Chemical Society. 133(24), 9506-9515, 2011-05. [JCR]　[WOS]
Lee YM, (Lim C*). Factors controlling the reactivity of zinc finger cores. Journal of the American Chemical Society. 133(22), 8691-703, 2011-05. [JCR]　[WOS]
Kuppuraj G, Sargsyan K, Hua YH, Merrill AR, (Lim C*). Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function. JOURNAL OF PHYSICAL CHEMISTRY B. 115(24), 7932-7939, 2011-05. [JCR]　[WOS]
Todor Dudev , (Carmay Lim*). Factors Controlling the Mechanism of NAD+ NonRedox Reactions. J. Am. Chem. Soc.. 132(46), 16533-16543, 2010-11. [JCR]　[WOS]
Chih Yuan Wu, Yao Chi Chen , (Carmay Lim*). A Structural-Alphabet-Based Strategy for Finding Structural Motifs Across Protein Families. Nucleic Acids Res.. 38(14), e150, 2010-08. [JCR]　[WOS]
Karen Sargsyan , (Carmay Lim*). Arrangement of 3D Structural Motifs in Ribosomal RNA. Nucleic Acids Res.. 38, 3512-3522, 2010-06. [JCR]　[WOS]
Yu-Ming Lee, C. Satheesan Babu, Yao Chi Chen, Milos Milcic, Yuanyuan Qu, (Carmay Lim*). Conserved Structural Motif for Recognizing Nicotinamide Adenine Dinucleotide in Poly(ADP-Ribose) Polymerases and ADP-Ribosylating Toxins: Implications for Structure-Based Drug Design. J. Med. Chem.. 53, 4038-4049, 2010-04. [JCR]　[WOS]
C. Satheesan Babu, (Carmay Lim*). Protein/Solvent Medium Effects on Mg2+ Carboxylate Interactions in Metalloenzymes. J. Am. Chem. Soc.. 132, 6290-6291, 2010-04. [JCR]　[WOS]
Todor Dudev, (Carmay Lim*). Factors Governing the Na+ vs. K+ Selectivity in Sodium Ion Channels. J. Am. Chem. Soc.. 132, 2321-2332, 2010-02. [JCR]　[WOS]
Yi-Ting Wang, Jon D. Wright, Lyudmila G. Doudeva, Hua-Ci Jhang, (Carmay Lim*) , Hanna S. Yuan*. Redesign of High-Affinity Nonspecific Nucleases with Altered Sequence Preference. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 131:17345–17353, 2009-12. [JCR]　[WOS]
Dudev T, Lim C*. Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations. JOURNAL OF PHYSICAL CHEMISTRY B. 113(34), 11754-64, 2009-08. [JCR]　[WOS]
Dudev T, Lim C*. Determinants of K+ vs Na+ selectivity in potassium channels. Journal of the American Chemical Society. 131(23), 8092-101, 2009-06. [JCR]　[WOS]
Yang PK, Lim C*. Strategies to model the near-solute solvent molecular density/polarization. Journal of computational chemistry. 30(5), 700-9, 2009-04. [JCR]　[WOS]
Lo CH, Chang YH, Wright JD, Chen SH, Kan D, Lim C*, Liang PH*. Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase. Journal of the American Chemical Society. 131(11), 4051-62, 2009-03. [JCR]　[WOS]
Gopi Kupparaj, Minko Dudev & Carmay Lim*. Factors Governing Metal–Ligand Bond Distances and Coordination Geometries of Metal Complexes. JOURNAL OF PHYSICAL CHEMISTRY B. 113:2952–2960, 2009-03. [JCR]　[WOS]
D. V. Sakharov and C. Lim. Force fields including charge transfer and local polarization effects: application to proteins containing multi/heavy metal ions. J Comput Chem. 30(2), 191-202, 2009-01. [JCR]　[WOS]
Y. C. Chen and C. Lim. Common physical basis of macromolecule-binding sites in proteins. Nucleic Acids Res. 36(22), 7078-7087, 2008. [JCR]　[WOS]
T. Dudev and C. Lim. Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Annu Rev Biophys. 37, 97-116, 2008. [JCR]　[WOS]
T. Y. Yang, T. Dudev and C. Lim. Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations. J Am Chem Soc. 130(12), 3844-3852, 2008. [JCR]　[WOS]
Y. M. Lee and C. Lim. Physical basis of structural and catalytic zn-binding sites in proteins. J Mol Biol. 379(3), 545-553, 2008. [JCR]　[WOS]
Y. C. Chen and C. Lim. Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res. 36(5), e29, 2008. [JCR]　[WOS]
P. K. Yang and C. Lim. Reformulation of maxwell’s equations to incorporate near-solute solvent structure. J Phys Chem B. 112(35), 10791-10794, 2008. [JCR]　[WOS]
P. K. Yang and C. Lim. The importance of excluded solvent volume effects in computing hydration free energies. J Phys Chem B. 112, 14863-14868, 2008. [JCR]　[WOS]
T. Dudev and C. Lim. All-electron calculations of the nucleation structures in metal-induced zinc-finger folding: role of the peptide backbone. J Am Chem Soc. 129(41), 12497-12504, 2007. [JCR]　[WOS]
M. Dudev and C. Lim. Discovering structural motifs using a structural alphabet: application to magnesium-binding sites. BMC Bioinformatics. 8, 106-118, 2007. [JCR]　[WOS]
T. Dudev and C. Lim. Effect of carboxylate-binding mode on metal binding and electivity in proteins. ACCOUNTS OF CHEMICAL RESEARCH. 40(1), 85-93, 2007. [JCR]　[WOS]
J. D. Wright and C. Lim. Mechanism of DNA-binding loss upon single-point mutation in p53. JOURNAL OF BIOSCIENCES. 32(5), 827-839, 2007. [JCR]　[WOS]
T. Kupka and C. Lim. Polarization-consistent versus correlation-consistent basic sets in predicting molecular and spectroscopic properties. J Phys Chem A. 111(10), 1927-1932, 2007. [JCR]　[WOS]
Y. C. Chen, C. Y. Wu and C. Lim. Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation. Proteins. 67(3), 671-680, 2007. [JCR]　[WOS]
T. Dudev, C. Lim. A DFT/CDM Study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates. J Am Chem Soc. 128, 1553-1561, 2006. [JCR]　[WOS]
T. Dudev, C. Lim. Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study. J Am Chem Soc. 128(32), 10541-10548, 2006. [JCR]　[WOS]
H. C. Tai, C. Lim. Computational studies of the coordination stereochemistry, bonding, and metal selectivity of mercury. J Phys Chem A. 110, 452-462, 2006. [JCR]　[WOS]
C. S. Babu, C. Lim. Empirical force fields for biologically active divalent metal cations in water. J Phys Chem A. 110, 691-699, 2006. [JCR]　[WOS]
M. Dudev, J. Wang, T. Dudev and C. Lim. Factor governing the metal coordination number in metal complexes from cambridge structural database analyses. J Phys Chem B. 110, 1889-1895, 2006. [JCR]　[WOS]
I. Tunell, C. Lim. Factors governing the metal coordination number in isolated group IA and IIA metal hydrates. Inorg Chem. 45, 4811-4819, 2006. [JCR]　[WOS]
D. C. Sullivan, C. Lim. Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition. JOURNAL OF PHYSICAL CHEMISTRY B. 110(33), 16707-16717, 2006. [JCR]　[WOS]
D. C. Sullivan, C. Lim. Toward absolute density of States calculations for proteins. J Phys Chem B. 110, 12125-12128, 2006. [JCR]　[WOS]
Y. L. Lin, Y. M. Lee and C. Lim. Differential effects of the Zn-His-Bkb vs Zn-His-[Asp/Glu] triad on Zn-core stability and reactivity. J Am Chem Soc. 1276, 11336-11347, 2005. [JCR]　[WOS]
T. Dudev, L. Y. Chang and C. Lim. Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study. J Am Chem Soc. 127, 4091-4103, 2005. [JCR]　[WOS]
D. V. Sakharov, C. Lim. Zn protein simulations including charge transfer and local polarization effects. J Am Chem Soc. 127, 4921-4929, 2005. [JCR]　[WOS]
D. Sullivan, C. Lim. Configurational Entropy of Proteins: Covariance Matrix versus Cumulative Distribution Calculations. J Chin Chem Soc. 51, 1209-1219, 2004. [JCR]　[WOS]
Y. L. Lin, C. Lim. Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study. J Am Chem Soc. 126, 2602-2612, 2004. [JCR]　[WOS]
T. Dudev, C. Lim. Monodentate versus Bidentate Carboxylate Binding in Magnesium and Calcium Proteins: What Are the Basic Principles?. J Phys Chem B. 108, 4546-4557, 2004. [JCR]　[WOS]
T. Dudev, C. Lim. Oxyanion Selectivity in Sulfate and Molybdate Transport Proteins: An ab Initio/CDM Study. J Am Chem Soc. 126, 10296-10304, 2004. [JCR]　[WOS]
C. S. Babu, T. Dudev, R. Casareno, J. A. Cowan and C. Lim. A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: application to E. coli ribonuclease H1. J Am Chem Soc. 125, 9318-9328, 2003. [JCR]　[WOS]
J.J.C. Sheu, T. Cheng, H. Y. Chen, C. Lim and T. W. Chang. Comparative Effects of Human Ig?and Igβ in Inducing Autoreactive Antibodies Against B Cells in Mice. J Immunol. 170, 1158-1166, 2003. [JCR]　[WOS]
T. Dudev, Y. L. Lin, M. Dudev and C. Lim. First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. J Am Chem Soc. 125, 3168-3180, 2003. [JCR]　[WOS]
T. Dudev, C. Lim. Metal Binding and Selectivity in Zinc Proteins. J Chin Chem Soc. 50, 1093-1102, 2003. [JCR]　[WOS]
T. Dudev, C. Lim. Principles governing Mg, Ca,, Zn binding, selectivity in proteins. Chem Rev. 103, 773-788, 2003. [JCR]　[WOS]
Y. L. Lin, N. Y. Chang and C. Lim. Factors governing intrinsic chemical reactivity differences between clavulanic and penicillanic acids. J Am Chem Soc. 124, 12042-12053, 2002. [JCR]　[WOS]
J. D. Wright, S. Y. Noskov and C. Lim. Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain. Nucleic Acids Res. 30, 1563-1574, 2002. [JCR]　[WOS]
T. Dudev, C. Lim. Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study. J Am Chem Soc. 124, 6759-6766, 2002. [JCR]　[WOS]
S. Y. Noskov, J. D. Wright and C. Lim. Long-Range Effects of Mutating R248 to Q/W in the p53 Core Domain. J Phys Chem B. 106, 13047-13057, 2002. [JCR]　[WOS]
P. K. Yang, C. Lim. Nonconvergence of the Solute Potential in an Infinite Solvent and Its Implications in Continuum Models. J Phys Chem B. 106, 12093-12096, 2002. [JCR]　[WOS]
C. S. Babu, P. K. Yang and C. Lim. On the Charge and Molecule Based Summations of Solvent Electrostatic Potentials and the Validity of Electrostatic Linear Response in Water. J Biol Phys. 28, 95-113, 2002. [JCR]　[WOS]
P. K. Yang, S. H. Liaw and C. Lim. Representing an Infinite Solvent System with a Rectangular Finite System Using Image Charges. J Phys Chem B. 106, 2973-2982, 2002. [JCR]　[WOS]
J. D. Wright, C. Lim. A fast method for predicting amino acid mutations that lead to unfolding. Protein Eng. 14, 479-486, 2001. [JCR]　[WOS]
S. Y. Noskov, C. Lim. Free energy decomposition of protein-protein interactions. Biophys J. 81, 737-750, 2001. [JCR]　[WOS]
C. S. Babu, C. Lim. Incorporating Nonlinear Solvent Response in Continuum Dielectric Models Using a Two-Sphere Description of the Born Radius. J Phys Chem A. 105, 5030-5036, 2001. [JCR]　[WOS]
T. Dudev, C. Lim. Metal Selectivity in Metalloproteins: Zn2+ vs Mg2+. J Phys Chem B. 105, 4446-4452, 2001. [JCR]　[WOS]
T. Dudev, C. Lim. Modeling Zn2+-Cysteinate Complexes in Proteins. J Phys Chem B. 105, 10709-10714, 2001. [JCR]　[WOS]
Y. Fan, C. Y. Wu, C. W. Chen, T. W. Chang and C. Lim. Preparing a human membrane and secreted protein-enriched cDNA library using PCR primers derived from a genomic database. Nucleic Acids Res. 29, E114, 2001. [JCR]　[WOS]
C. S. Babu, C. Lim. Solvation free energies of polar molecular solutes: application of the two-sphere born radius in continuum models of solvation. J Chem Phys. 114, 889-899, 2001. [JCR]　[WOS]
K. Y. Lin, J. Wright and C. Lim. Conformational analysis of long spacers in PROSITE patterns. J Mol Biol. 299, 537-548, 2000. [JCR]　[WOS]
G. H. Hakimelahi, A. A. Moosavi-Movahedi, S. C. Tsay, F. Y. Tsai, J. D. Wright, T. Dudev, S. Hakimelahi and C. Lim. Design, synthesis, and SAR of novel carbapenem antibiotics with high stability to Xanthomonas maltophilia oxyiminocephalosporinase type II. J Med Chem. 43, 3632-3640, 2000. [JCR]　[WOS]
T. Dudev, C. Lim. Metal Binding in Proteins: The Effect of the Dielectric Medium. J Phys Chem B. 104, 3692-3694, 2000. [JCR]　[WOS]
T. Dudev, C. Lim. Tetrahedral vs Octahedral Zinc Complexes with Ligands of Biological Interest: A DFT/CDM Study. J Am Chem Soc. 122, 11146-11153, 2000. [JCR]　[WOS]
S. Babu, C. Lim. A new interpretation of the effective born radius from simulation and experiment. Chem Phys Lett. 310, 225-228, 1999. [JCR]　[WOS]
T. Dudev, J. Cowan and C. Lim. Competitive Binding in Magnesium Coordination Chemistry: Water versus Ligands of Biological Interest. J Am Chem Soc. 121, 7665-7673, 1999. [JCR]　[WOS]
M. Philippopoulos, C. Lim. Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI. Proteins. 36, 87-110, 1999. [JCR]　[WOS]
T. Dudev, C. Lim. Incremental Binding Free Energies in Mg2+ Complexes: A DFT Study. J Phys Chem A. 103, 8093-8100, 1999. [JCR]　[WOS]
C. Lim. Ring strain vs. solvent effects in phosphate base hydrolysis. Phosphorus, Sulfur and Silicon. 144-146, 769-773, 1999. [JCR]　[WOS]
C. S. Babu, C. Lim. Theory of Ionic Hydration: Insights from Molecular Dynamics Simulations and Experiment. J Phys Chem B. 103, 7958-7968, 1999. [JCR]　[WOS]
N. Y. Chang, C. Lim. Factors Governing the Enhanced Reactivity of Five-Membered Cyclic Phosphate Esters. J Am Chem Soc. 120, 2156-2167, 1998. [JCR]　[WOS]
J. D. Wright, C. Lim. Prediction of an anti-IgE binding site on IgE. PROTEIN ENGINEERING. 11, 421-427, 1998. [JCR]　[WOS]
M. Philippopoulos, A. M. Mandel, A. G. Palmer, 3rd and C. Lim. Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins. 28, 481-493, 1997. [JCR]　[WOS]
N. Y. Chang, C. Lim. An ab Initio Study of Nucleophilic Attack of Trimethyl Phosphate: Factors Influencing Site Reactivity. J Phys Chem A. 101, 8706-8713, 1997. [JCR]　[WOS]
L. P. Wang, C. Lim, Y. Kuan, C. L. Chen, H. F. Chen and K. King. Positive charge at position 549 is essential for phosphatidylinositol 4,5-bisphosphate-hydrolyzing but not phosphatidylinositol-hydrolyzing activities of human phospholipase C delta1. J Biol Chem. 271, 24505-24516, 1996. [JCR]　[WOS]
M. H. Feng, S. L. Chan, Y. Xiang, C. P. Huber and C. Lim. The binding mode of an E-64 analog to the active site of cathepsin B. Protein Eng. 9, 977-986, 1996. [JCR]　[WOS]
Tse Wen Chang*, Hsing-Mao Chu, Chien-Jen Lin, Maria Chen, Yu-ming Lee, and Carmay Lim. A platform for developing new drugs with targeting and effector functions. . , 2017-01. [JCR]　[WOS]
Wei-Ming Tu, Chen Chih-Cheng, and Carmay Lim*. Biochemical basis of vitamin B12 deficiency induced myelin-damage and neuropathic pain. . , 2017-01. [JCR]　[WOS]
C. Satheesan Babu* & Carmay Lim*. NADPH_. . , 2017-01. [JCR]　[WOS]
Chi Chen*, Yu-Hsien Chen, Jon D. Wright, Yi-Shuian Huang, and Carmay Lim*. PPIK: Detecting protein-protein interface key residues. . , 2017-01. [JCR]　[WOS]
Jon D. Wright, Chou-Long Huang*, and Carmay Lim*. Structural basis for the recognition of the 2,3-sialyllactose group on GM1/GM3 by the Klotho KL1 domain. . , 2017-01. [JCR]　[WOS]

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