| Hassan, B. A., Liu, Z. A., Milicaj, J., Kim, M. S., Tyson, M., Sham, Y. Y., Taylor, E. A. (2022). Kinetic Characterization and Computational Modeling of Escherichia coli Heptosyltransferase II: Exploring the Role of Protein Dynamics in Catalysis for GT-B Glycosyltransferase. Biochemistry, 61(15), 1572-1584. PMID: 35861590 doi: 10.1021/acs.biochem.2c00329 |
| Milicaj, J., Hassan, B. A., Cote, J. M., Ramirez-Mondragon, C. A., Jaunbocus, N., Rafalowski, A., Patel, K. R., Castro, C. D., Muthyala, R., Sham, Y. Y., Taylor, E. A. (2022). Discovery of first-in-class nanomolar inhibitors of heptosyltransferase I reveals a new aminoglycoside target and potential alternative mechanism of action. Scientific reports, 12(1), 7302. PMID: 35508636 PMCID: PMC9068772 doi: 10.1038/s41598-022-10776-x |
| Milicaj*, J., Dodda*, V. R., Patel, K. R., Rodriguez Aragon, I., O'Connell, T., Muthyala, R. (Corresponding Author), Taylor, E. A. (Corresponding Author), Sham, Y. Y. (Corresponding Author) (2022). Facile and adaptable synthesis of a Prazosin analogue library: Bringing medicinal chemistry into the undergraduate curriculum. JOURNAL OF CHEMICAL EDUCATION, 99, 1428-1434. doi: doi.org/10.1021/acs.jchemed.1c00822 |
| Hassan, B. A., Milicaj, J., Ramirez-Mondragon, C. A., Sham, Y. Y., Taylor, E. A. (2022). Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes. Journal of chemical information and modeling, 62(2), 324-339. PMID: 34967618 PMCID: PMC8864558 doi: 10.1021/acs.jcim.1c00868 |
| Ampudia-Mesias, E., Puerta-Martinez, F., Bridges, M., Zellmer, D., Janeiro, A., Strokes, M., Sham, Y. Y., Taher, A., Castro, M., Moertel, C. L., Pluhar, G. E., Olin, M. R. (2021). CD200 Immune-Checkpoint Peptide Elicits an Anti-glioma Response Through the DAP10 Signaling Pathway. NEUROTHERAPEUTICS, 18(3), 1980-1994. doi: 10.1007/s13311-021-01038-1 |
| Ramirez-Mondragon, C. A., Nguyen, M. E., Milicaj, J., Hassan, B. A., Tucci, F. J., Muthyala, R., Gao, J., Taylor, E. A., Sham, Y. Y. (2021). Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(9). doi: 10.3390/ijms22094619 |
| Shin, W. S., Nguyen, M. E., Bergstrom, A., Jennings, I. R., Crowder, M. W., Muthyala, R., Sham, Y. Y. (2021). Fragment-based screening and hit-based substructure search: Rapid discovery of 8-hydroxyquinoline-7-carboxylic acid as a low-cytotoxic, nanomolar metallo beta-lactamase inhibitor. CHEMICAL BIOLOGY & DRUG DESIGN, 98(4), 481-492. doi: 10.1111/cbdd.13912 |
| Ortiz-Cordero, C., Magli, A., Dhoke, N. R., Kuebler, T., Selvaraj, S., Oliveira, Nelio A. J., Zhou, H., Sham, Y. Y., Bang, A. G., Perlingeiro, Rita C. R. (2021). NAD plus enhances ribitol and ribose rescue of alpha-dystroglycan functional glycosylation in human FKRP-mutant myotubes. ELIFE, 10. doi: 10.7554/eLife.65443 |
| Xiong, Z., Mesias, E. A., Pluhar, G. E., Rathe, S. K., Largaespada, D. A., Sham, Y. Y., Moertel, C. L., Olin, M. R. (2020). CD200 Checkpoint Reversal: A Novel Approach to Immunotherapy. CLINICAL CANCER RESEARCH, 26(1), 232-241. doi: 10.1158/1078-0432.CCR-19-2234 |
| Cote, J. M., Hecht, Cody J. S., Patel, K. R., Ramirez-Mondragon, C. A., Sham, Y. Y., Taylor, E. A. (2020). Opposites Attract: Escherichia coli Heptosyltransferase I Conformational Changes Induced by Interactions between the Substrate and Positively Charged Residues. BIOCHEMISTRY, 59(34), 3135-3147. doi: 10.1021/acs.biochem.9b01005 |
| Sahu, B. S., Rodriguez, P., Nguyen, M. E., Han, R., Cero, C., Razzoli, M., Piaggi, P., Laskowski, L. J., Pavlicev, M., Muglia, L., Mahata, S. K., O'Grady, S., McCorvy, J. D., Baier, L. J., Sham, Y. Y., Bartolomucci, A. (2019). Peptide/Receptor Co-evolution Explains the Lipolytic Function of the Neuropeptide TLQP-21. CELL REPORTS, 28(10), 2567-+. doi: 10.1016/j.celrep.2019.07.101 |
| Zafar, S., Nguyen, M. E., Muthyala, R., Jabeen, I., Sham, Y. Y. (2019). Modeling and Simulation of hGAT1: A Mechanistic Investigation of the GABA Transport Process. Computational and Structural Biotechnology Journal, 17, 61-69. doi: 10.1016/j.csbj.2018.12.003 |
| Seiler, C. L., Fernandez, J., Koerperich, Z., Andersen, M. P., Kotandeniya, D., Nguyen, M. E., Sham, Y. Y., Tretyakova, N. Y. (2018). Maintenance DNA Methyltransferase Activity in the Presence of Oxidized Forms of 5-Methylcytosine: Structural Basis for Ten Eleven Translocation-Mediated DNA Demethylation. Biochemistry, 57(42), 6061-6069. doi: 10.1021/acs.biochem.8b00683 |
| Cong, H., Zhao, X., Castle, B. T., Pomeroy, E. J., Zhou, B., Lee, J., Wang, Y., Bian, T., Miao, Z., Zhang, W., Sham, Y. Y., Odde, D. J., Eckfeldt, C. E., Xing, C., Zhuang, C. (2018). An Indole-Chalcone Inhibits Multidrug-Resistant Cancer Cell Growth by Targeting Microtubules. Molecular Pharmaceutics, 15(9), 3892-3900. doi: 10.1021/acs.molpharmaceut.8b00359 |
| Vetter, A. D., Houang, E. M., Sell, J. J., Thompson, B. R., Sham, Y. Y., Metzger, J. M. (2018). TnI Structural Interface with the N-Terminal Lobe of TnC as a Determinant of Cardiac Contractility. Biophysical Journal, 114(7), 1646-1656. doi: 10.1016/j.bpj.2018.02.015 |
| Zhou, Y., Wu, Y., Pokholenko, O., Grimsrud, M., Sham, Y., Papper, V., Marks, R., Steele, T. (2018). Aptamer adaptive binding assessed by stilbene photoisomerization towards regenerating aptasensors. Sensors and Actuators, B: Chemical, 257, 245-255. doi: 10.1016/j.snb.2017.10.135 |
| Kotandeniya, D., Seiler, C. L., Fernandez, J., Pujari, S. S., Curwick, L., Murphy, K., Wickramaratne, S., Yan, S., Murphy, D., Sham, Y. Y., Tretyakova, N. Y. (2018). Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? Chemical Communications, 54(9), 1061-1064. doi: 10.1039/c7cc06867k |
| Houang, E. M., Bates, F. S., Sham, Y. Y., Metzger, J. M. (2017). All-Atom Molecular Dynamics-Based Analysis of Membrane-Stabilizing Copolymer Interactions with Lipid Bilayers Probed under Constant Surface Tensions. Journal of Physical Chemistry B, 121(47), 10657-10664. doi: 10.1021/acs.jpcb.7b08938 |
| Houang, E. M., Haman, K. J., Kim, M., Zhang, W., Lowe, D. A., Sham, Y. Y., Lodge, T. P., Hackel, B. J., Bates, F. S., Metzger, J. M. (2017). Chemical End Group Modified Diblock Copolymers Elucidate Anchor and Chain Mechanism of Membrane Stabilization. Molecular Pharmaceutics, 14(7), 2333-2339. doi: 10.1021/acs.molpharmaceut.7b00197 |
| Cote, J. M., Ramirez-Mondragon, C. A., Siegel, Z. S., Czyzyk, D. J., Gao, J., Sham, Y. Y., Mukerji, I., Taylor, E. A. (2017). The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli. Biochemistry, 56(6), 886-895. doi: 10.1021/acs.biochem.6b00850 |
| Shin, W. S., Bergstrom, A., Bonomo, R. A., Crowder, M. W., Muthyala, R., Sham, Y. Y. (2017). Discovery of 1-Hydroxypyridine-2(1H)-thione-6-carboxylic Acid as a First-in-Class Low-Cytotoxic Nanomolar Metallo β-Lactamase Inhibitor. ChemMedChem, 12(11), 845-849. doi: 10.1002/cmdc.201700182 |
| Wickramaratne, S., Ji, S., Mukherjee, S., Su, Y., Pence, M. G., Lior-Hoffmann, L., Fu, I., Broyde, S., Guengerich, F. P., Distefano, M., Schãrer, O. D., Sham, Y. Y., Tretyakova, N. (2016). Bypass of DNA-protein cross-links conjugated to the 7-deazaguanine position of DNA by translesion synthesis polymerases. Journal of Biological Chemistry, 291(45), 23589-23603. doi: 10.1074/jbc.M116.745257 |
| Peng, Z., Xu, W. W., Sham, Y., Lam, H., Sun, D., Cheng, L., Rasic, N. F., Guan, Q., James, A. A., Simons, F. E.R. (2016). Mosquito salivary allergen Aed a 3: Cloning, comprehensive molecular analysis, and clinical evaluation. Allergy: European Journal of Allergy and Clinical Immunology, 71(5), 621-628. doi: 10.1111/all.12812 |
| Akgün, E., Javed, M. I., Lunzer, M. M., Powers, M. D., Sham, Y. Y., Watanabe, Y., Portoghese, P. S. (2015). Inhibition of inflammatory and neuropathic pain by targeting a Mu opioid receptor/chemokine receptor5 heteromer (MOR-CCR<inf>5</inf>). Journal of Medicinal Chemistry, 58(21), 8647-8657. doi: 10.1021/acs.jmedchem.5b01245 |
| Muthyala, R., Shin, W. S., Xie, J., Sham, Y. Y. (2015). Discovery of 1-hydroxypyridine-2-thiones as selective histone deacetylase inhibitors and their potential application for treating leukemia. Bioorganic and Medicinal Chemistry Letters, 25(19), 4320-4324. doi: 10.1016/j.bmcl.2015.07.065 |
| Muthyala, R., Rastogi, N., Shin, W. S., Peterson, M. L., Sham, Y. Y. (2014). Cell permeable vanX inhibitors as vancomycin re-sensitizing agents. Bioorganic and Medicinal Chemistry Letters, 24(11), 2535-2538. doi: 10.1016/j.bmcl.2014.03.097 |
| Thompson, B. R., Houang, E. M., Sham, Y. Y., Metzger, J. M. (2014). Molecular determinants of cardiac myocyte performance as conferred by isoform-specific tni residues. Biophysical Journal, 106(10), 2105-2114. doi: 10.1016/j.bpj.2014.04.017 |
| Zhuang, C., Narayanapillai, S., Zhang, W., Sham, Y. Y., Xing, C. (2014). Rapid identification of Keap1-Nrf2 small-molecule inhibitors through structure-based virtual screening and hit-based substructure search. Journal of Medicinal Chemistry, 57(3), 1121-1126. doi: 10.1021/jm4017174 |
| Zhuang, C., Sheng, C., Shin, W. S., Wu, Y., Li, J., Yao, J., Dong, G., Zhang, W., Sham, Y. Y., Miao, Z., Zhang, W. (2014). A novel drug discovery strategy: Mechanistic investigation of an enantiomeric antitumor agent targeting dual p53 and NF-κB pathways. Oncotarget, 5(21), 10830-10839. doi: 10.18632/oncotarget.2521 |
| Zhou, W., Chen, F., Klyachkin, Y., Sham, Y. Y., Geraghty, R. J. (2014). Mutations in the amino terminus of herpes simplex virus type 1 gL can reduce cell-cell fusion without affecting gH/gL trafficking. Journal of Virology, 88(1), 739-744. doi: 10.1128/JVI.02383-13 |
| Ferreira, R., Artali, R., Benoit, A., Gargallo, R., Eritja, R., Ferguson, D. M., Sham, Y. Y., Mazzini, S. (2013). Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines. PLoS ONE, 8(3). doi: 10.1371/journal.pone.0057701 |
| Sirivolu, V. R., Vernekar, S. K., Marchand, C., Naumova, A., Chergui, A., Renaud, A., Stephen, A. G., Chen, F., Sham, Y. Y., Pommier, Y., Wang, Z. (2012). 5-Arylidenethioxothiazolidinones as Inhibitors of Tyrosyl-DNA Phosphodiesterase i. Journal of Medicinal Chemistry, 55(20), 8671-8684. doi: 10.1021/jm3008773 |
| Palpant, N. J., Houang, E. M., Sham, Y. Y., Metzger, J. M. (2012). PH-responsive titratable inotropic performance of histidine-modified cardiac troponin i. Biophysical Journal, 102(7), 1570-1579. doi: 10.1016/j.bpj.2012.01.024 |
| Chen, Y. L., Tang, J., Kesler, M. J., Sham, Y. Y., Vince, R., Geraghty, R. J., Wang, Z. (2012). The design, synthesis and biological evaluations of C-6 or C-7 substituted 2-hydroxyisoquinoline-1,3-diones as inhibitors of hepatitis C virus. Bioorganic and Medicinal Chemistry, 20(1), 467-479. doi: 10.1016/j.bmc.2011.10.058 |
| Wilson, D. J., Shi, C., Duckworth, B. P., Muretta, J. M., Manjunatha, U., Sham, Y. Y., Thomas, D. D., Aldrich, C. C. (2011). A continuous fluorescence displacement assay for BioA: An enzyme involved in biotin biosynthesis. Analytical Biochemistry, 416(1), 27-38. doi: 10.1016/j.ab.2011.05.003 |
| Li, L., Sham, Y. Y., Bikadi, Z., Elmquist, W. F. (2011). pH-dependent transport of pemetrexed by breast cancer resistance protein. Drug Metabolism and Disposition, 39(9), 1478-1485. doi: 10.1124/dmd.111.039370 |
| Tang, J., Maddali, K., Dreis, C. D., Sham, Y. Y., Vince, R., Pommier, Y., Wang, Z. (2011). 6-Benzoyl-3-hydroxypyrimidine-2,4-diones as dual inhibitors of HIV reverse transcriptase and integrase. Bioorganic and Medicinal Chemistry Letters, 21(8), 2400-2402. doi: 10.1016/j.bmcl.2011.02.069 |
| Tang, J., Maddali, K., Metifiot, M., Sham, Y. Y., Vince, R., Pommier, Y., Wang, Z. (2011). 3-Hydroxypyrimidine-2,4-diones as an Inhibitor Scaffold of HIV Integrase. Journal of Medicinal Chemistry, 54(7), 2282-2292. doi: 10.1021/jm1014378 |
| Tang, J., Maddali, K., Dreis, C. D., Sham, Y. Y., Vince, R., Pommier, Y., Wang, Z. (2011). N-3 hydroxylation of pyrimidine-2,4-diones yields dual inhibitors of HIV reverse transcriptase and integrase. ACS Medicinal Chemistry Letters, 2(1), 63-67. doi: 10.1021/ml1002162 |
| Chen, L., Petrelli, R., Gao, G., Wilson, D. J., McLean, G. T., Jayaram, H. N., Sham, Y. Y., Pankiewicz, K. W. (2010). Dual inhibitors of inosine monophosphate dehydrogenase and histone deacetylase based on a cinnamic hydroxamic acid core structure. Bioorganic and Medicinal Chemistry, 18(16), 5950-5964. doi: 10.1016/j.bmc.2010.06.081 |
| Palpant, N. J., Houang, E. M., Delport, W., Hastings, K. E., Onufriev, A. V., Sham, Y. Y., Metzger, J. M. (2010). Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations. Physiological Genomics, 42(2), 287-299. doi: 10.1152/physiolgenomics.00033.2010 |
| Chen, L., Wilson, D. J., Xu, Y., Aldrich, C. C., Felczak, K., Sham, Y. Y., Pankiewicz, K. W. (2010). Triazole-linked inhibitors of inosine monophosphate dehydrogenase from human and mycobacterium tuberculosis. Journal of Medicinal Chemistry, 53(12), 4768-4778. doi: 10.1021/jm100424m |
| Tang, J., Maddali, K., Pommier, Y., Sham, Y. Y., Wang, Z. (2010). Scaffold rearrangement of dihydroxypyrimidine inhibitors of HIV integrase: Docking model revisited. Bioorganic and Medicinal Chemistry Letters, 20(11), 3275-3279. doi: 10.1016/j.bmcl.2010.04.048 |
| Lu, D., Sham, Y. Y., Vince, R. (2010). Design, asymmetric synthesis, and evaluation of pseudosymmetric sulfoximine inhibitors against HIV-1 protease. Bioorganic and Medicinal Chemistry, 18(5), 2037-2048. doi: 10.1016/j.bmc.2010.01.020 |
| Petrelli, R., Sham, Y. Y., Chen, L., Felczak, K., Bennett, E., Wilson, D., Aldrich, C., Yu, J. S., Cappellacci, L., Franchetti, P., Grifantini, M., Mazzola, F., Di Stefano, M., Magni, G., Pankiewicz, K. W. (2009). Selective inhibition of nicotinamide adenine dinucleotide kinases by dinucleoside disulfide mimics of nicotinamide adenine dinucleotide analogues. Bioorganic and Medicinal Chemistry, 17(15), 5656-5664. doi: 10.1016/j.bmc.2009.06.013 |
| Cohen, D. N., Sham, Y. Y., Haugstad, G. D., Xiang, Y., Rossmann, M. G., Anderson, D. L., Popham, D. L. (2009). Shared Catalysis in Virus Entry and Bacterial Cell Wall Depolymerization. Journal of Molecular Biology, 387(3), 607-618. doi: 10.1016/j.jmb.2009.02.001 |
| Raza, A., Sham, Y. Y., Vince, R. (2008). Design and synthesis of sulfoximine based inhibitors for HIV-1 protease. Bioorganic and Medicinal Chemistry Letters, 18(20), 5406-5410. doi: 10.1016/j.bmcl.2008.09.044 |
| Nesmelova, I. V., Sham, Y., Gao, J., Mayo, K. H. (2008). CXC and CC chemokines form mixed heterodimers: Association free energies from molecular dynamics simulations and experimental correlations. Journal of Biological Chemistry, 283(35), 24155-24166. doi: 10.1074/jbc.M803308200 |
| Duckworth, B. P., Chen, Y., Wollack, J. W., Sham, Y., Mueller, J. D., Taton, T. A., Distefano, M. D. (2007). A universal method for the preparation of covalent protein-DNA conjugates for use in creating protein nanostructures. Angewandte Chemie - International Edition, 46(46), 8819-8822. doi: 10.1002/anie.200701942 |
| Chou, T. F., Sham, Y. Y., Wagner, C. R. (2007). Impact of the C-terminal loop of histidine triad nucleotide binding protein 1 (Hint1) on substrate specificity. Biochemistry, 46(45), 13074-13079. doi: 10.1021/bi701244h |
| Xing, C., Wang, L., Tang, X. H., Sham, Y. Y. (2007). Development of selective inhibitors for anti-apoptotic Bcl-2 proteins from BHI-1. Bioorganic and Medicinal Chemistry(5), 2167-2176. doi: 10.1016/j.bmc.2006.12.020 |
| Li, M., He, Z., Ermakova, S., Zheng, D., Tang, F., Cho, Y. Y., Zhu, F., Ma, W. Y., Sham, Y., Rogozin, E. A., Bode, A. M., Cao, Y., Dong, Z. (2007). Direct inhibition of insulin-like growth factor-I receptor kinase activity by (-)-epigallocatechin-3-gallate regulates cell transformation. Cancer Epidemiology Biomarkers and Prevention, 16(3), 598-605. doi: 10.1158/1055-9965.EPI-06-0892 |
| Ma, L., Sham, Y. Y., Walters, K. J., Towle, H. C. (2007). A critical role for the loop region of the basic helix-loop-helix/ leucine zipper protein Mlx in DNA binding and glucose-regulated transcription. Nucleic Acids Research, 35(1), 35-44. doi: 10.1093/nar/gkl987 |
| Kumar, V., Locuson, C. W., Sham, Y. Y., Tracy, T. S. (2006). Amiodarone analog-dependent effects on CYP2C9-mediated metabolism and kinetic profiles. Drug Metabolism and Disposition, 34(10), 1688-1696. doi: 10.1124/dmd.106.010678 |
| Zhang, Y., Sham, Y. Y., Rajamani, R., Gao, J., Portoghese, P. S. (2005). Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system. ChemBioChem, 6(5), 853-859. doi: 10.1002/cbic.200400207 |
| Nesmelova, I. V., Sham, Y., Dudek, A. Z., Van Eijk, L. I., Wu, G., Slungaard, A., Mortari, F., Griffioen, A. W., Mayo, K. H. (2005). Platelet factor 4 and interleukin-8 CXC chemokine heterodimer formation modulates function at the quaternary structural level. Journal of Biological Chemistry, 280(6), 4948-4958. doi: 10.1074/jbc.M405364200 |
| Fitch, B. G., Germain, R. S., Mendell, M., Pitera, J., Pitman, M., Rayshubskiy, A., Sham, Y., Suits, F., Swope, W., Ward, T. J.C., Zhestkov, Y., Zhou, R. (2003). Blue Matter, an application framework for molecular simulation on Blue Gene. Journal of Parallel and Distributed Computing, 63(7-8), 759-773. doi: 10.1016/S0743-7315(03)00084-4 |
| Sham, Y. Y., Ma, B., Tsai, C. J., Nussinov, R. (2002). Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway. 46(3), 308-320. doi: 10.1002/prot.10040 |
| Tsai, C. J., Ma, B., Sham, Y. Y., Kumar, S., Wolfson, H. J., Nussinov, R. (2001). A hierarchical, building-block-based computational scheme for protein structure prediction. IBM Journal of Research and Development, 45(3-4), 513-523. https://api.elsevier.com/content/abstract/scopus_id/0035327482 |
| Allen, F., Almasi, G., Andreoni, W., Beece, D., Berne, B. J., Bright, A., Brunheroto, J., Cascaval, C., Castanos, J., Coteus, P., Crumley, P., Curioni, A., Denneau, M., Donath, W., Eleftheriou, M., Fitch, B., Fleischer, B., Georgiou, C. J., Germain, R., Giampapa, M., Gresh, D., Gupta, M., Haring, R., Ho, H., Hochschild, P., Hummel, S., Jonas, T., Lieber, D., Martyna, G., Maturu, K., Moreira, J., Newns, D., Newton, M., Philhower, R., Picunko, T., Pitera, J., Pitman, M., Rand, R., Royyuru, A., Salapura, V., Sanomiya, A., Shah, R., Sham, Y., Singh, S., Snir, M., Suits, F., Swetz, R., Swope, W. C., Vishnumurthy, N., Ward, T. J.C., Warren, H., Zhou, R. (2001). Blue Gene: A vision for protein science using a petaflop supercomputer. IBM Systems Journal, 40(2), 310-327. doi: 10.1147/sj.402.0310 |
| Kumar, S., Sham, Y. Y., Tsai, C. J., Nussinov, R. (2001). Protein folding and function: The N-terminal fragment in adenylate kinase. Biophysical Journal, 80(5), 2439-2454. doi: 10.1016/S0006-3495(01)76213-3 |
| Villà, J., Štrajbl, M., Glennon, T. M., Sham, Y. Y., Chu, Z. T., Warshel, A. (2000). How important are entropic contributions to enzyme catalysis? Proceedings of the National Academy of Sciences of the United States of America, 97(22), 11899-11904. doi: 10.1073/pnas.97.22.11899 |
| Sham, Y. Y., Chu, Z. T., Tao, H., Warshel, A. (2000). Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins: Structure, Function and Genetics, 39(4), 393-407. doi: 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.0.CO;2-H |
| Strajbl, M., Sham, Y. Y., Villà, J., Chu, Z. T., Warshel, A. (2000). Calculations of Activation Entropies of Chemical Reactions in Solution. Journal of Physical Chemistry B, 104(18), 4578-4584. https://api.elsevier.com/content/abstract/scopus_id/0000997465 |
| Sham, Y. Y., Muegge, I., Warshel, A. (1999). Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center. Proteins: Structure, Function and Genetics, 36(4), 484-500. doi: 10.1002/(SICI)1097-0134(19990901)36:4<484::AID-PROT13>3.0.CO;2-R |
| Sham, Y. Y., Warshel, A. (1998). The surface constraint all atom model provides size independent results in calculations of hydration free energies. Journal of Chemical Physics, 109(18), 7940-7944. doi: 10.1063/1.477441 |
| Sham, Y. Y., Muegge, I., Warshel, A. (1998). The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophysical Journal, 74(4), 1744-1753. doi: 10.1016/S0006-3495(98)77885-3 |
| Sham, Y. Y., Chu, Z. T., Warshel, A. (1997). Consistent calculations of pK<inf>a</inf>'s of ionizable residues in proteins: Semi-microscopic and microscopic approaches. Journal of Physical Chemistry B, 101(22), 4458-4472. https://api.elsevier.com/content/abstract/scopus_id/0000671518 |
| Sham, Y. Y., Joens, J. A. (1995). Temperature dependent near UV molar absorptivities of several small aldehydes in aqueous solution. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 51(2), 247-251. doi: 10.1016/0584-8539(94)E0089-S |
This will describe Yuk's area of research one