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Yuk Sham - Research

Complete Publication List

  1. PH responsive titratable performance of histidine-modified cardiac troponin I attributed to imidazole ionization. Palpant NJ, Houang EM, Sham YY, Metzger JM. Biophysical Journal (accepted). 

  2. Consistent pKa calculation in proteins. Chen F, Shin WS, Yoon HW, Sham YY. A course on biomolecular simulations, Villà-Freixa J, Ed., Huygens Editorial, Barcelona, Spain. (accepted).

  3. The Design, Synthesis and Biological Evaluations of C-6 or C-7 Substituted 2-Hydroxylisoquinoline-1,3-diones as Inhibitors of Hepatitis C Virus. Chen YL, Tang J, Kesler MJ, Sham YY, Vince R, Geraghty RJ and Wang Z. Bioorganic and Medicinal Chemistry, 20: 467–479 (2012). Abstract

  4. PH-dependent transport of pemetrexed by breast cancer resistance protein, Li l, Sham YY, Bikadi Z, Elmquist WF, Drug Metabolism and Disposition, 39: 1478-1485 (2011). (Cover Article)  Abstract

  5. A continuous fluorescence displacement assay for BioA: An enzyme involved in biotin. Wilson DJ, Shi C, Duckworth BP, Muretta JM, Manjunatha U, Sham YY, Thomas DD, Aldrich CC. Analytical Biochemistry, 416: 27-38 (2011). Abstract

  6. 6-Benzoyl-3-hydroxypyrimidine-2,4-diones as dual inhibitors of HIV reverse transcriptase and integrase. Tang J, Maddali K, Dreis CD, Sham YY, Vince R, Pommier Y, Wang Z. Bioorganic & Medicinal Chemistry Letters, 21:2400-2402 (2011). Abstract

  7. 3-Hyroxypyrimidine-2,4-diones as novel scaffold for HIV integrase inhibitor design. Tang J, Maddali K, Metifiot M, Sham YY, Vince R, Pommier Y, Wang Z. Journal of Medicinal Chemistry, 54:2282-92 (2011). Abstract

  8. N-3 hydroxylation of pyrimidine-2,4-diones yields dual inhibitors of HIV reverse transcriptase and integrase. Tang J, Maddali K, Dreis CD, Sham YY, Vince R, Pommier Y, Wang Z. ACS Medicinal Chemistry Letters 2: 63-67 (2011). Abstract

  9. Dual inhibitors of inosine monophosphate dehydrogenase and histone deacetylase based on a cinnamic hydroxamic acid core structure. Chen L, Petrelli R, Gao G, Wilson D, McLean GT, Jayaram HN, Sham YY, Pankiewicz KW. Bioorganic and Medicinal Chemistry 18: 5950-5964 (2010). Abstract

  10. Triazole-linked inhibitors of inosine monophosphate dehydrogenase from human and Mycobacterium tuberculosis. Chen L, Wilson DJ, Xu Y, Aldrich CC, Felczak K, Sham YY, Pankiewicz KW. Journal of Medicinal Chemistry 53: 4768-4778 (2010). Abstract

  11. Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutation. Palpant NJ, Houang EM, Delport W, Hastings K, Onufrieve AV, Sham YY, Metzger JM. Physiological Genomics 42: 287-299 (2010). Abstract

  12. Scaffold rearrangement of dihydroxypyrimidine inhibitors of HIV integrase: Docking model revisited. Tang J, Maddali K, Pommier Y, Sham YY, Wang Z. Bioorganic and Medicinal Chemistry Letters 20: 3275-3279 (2010). Abstract

  13. Design, asymmetric synthesis and evaluation of pseudosymmetric sulfoximine inhibitors against HIV-1 protease. Lu D, Sham YY, Vince R. Bioorganic and Medicinal Chemistry 18: 2037-2048 (2010). Abstract

  14. Selective inhibition of NAD kinases by dinucleoside disulfide NAD mimics. Petrelli R, Sham YY, Chen L, Felczak K, Bennett E, Wilson D, Aldrich C, Yu JS, Cappellacci L, F ranchetti P, Grifantini M, Mazzola F, Di Stefano M, Magni G, Pankiewicz K. Bioorganic and Medicinal Chemistry 17: 5656-5664 (2009). Abstract

  15. Shared catalysis in virus entry and bacterial cell wall depolymerization. Cohen DN, Sham YY, Haugstad GD, Xiang Y, Rossmann MG, Anderson DL, Popham DL. Journal of Molecular Biology 387: 607-618 (2009). Abstract

  16. Design and synthesis of asymmetric sulfoximine inhibitors for HIV-1 protease. Raza A, Sham YY, Vince R.  Bioorganic & Medicinal Chemistry Letters, 18(20): 5406-5410 (2008). Abstract

  17. CXC and CC-chemokines form mixed heterodimers: Association free energies from MD simulations and experimental correlations. Nesmelova IV, Sham Y, Gao J, Mayo KH.  Journal of Biological Chemistry, 283(35): 24155-66 (2008). Abstract

  18. Impact of the C terminal loop of histidine triad nucleotide binding protein1 (Hint1) on substrate specificity. Chou TF, Sham YY, Wagner CR. Biochemistry, 46(45): 13074-79 (2007). Abstract

  19. A universal method for the preparation of covalent protein DNA conjugates for use in creating protein nanostructures. Duckworth BP, Chen Y, Wollack JW, Sham YY, Mueller JD, Taton TA, Distefano MD. Angewandte Chemie International Edition, 46(46): 8819-22 (2007). Abstract

  20. Direct inhibition of insulin-like growth factor-I receptor kinase activity by (-)-epigallocatechin-3-gallate regulates cell transformation. Li M, He Z, Ermakova S, Zheng D, Tang F, Cho YY, Zhu F, Ma WY, Sham YY, Rogozin EA, Bode AM, Cao Y, Dong Z. Cancer Epidemiology Biomarkers Prevention, 16(3): 598-605 (2007). Abstract

  21. Development of selective inhibitors for anti apoptotic Bcl 2 proteins from BHI 1. Xing C, Wang L, Tang X, Sham YY. Bioorganic and Medicinal Chemistry, 15(5): 2167-76 (2007). Abstract

  22. A critical role for the loop region of the basic helix-loop-helix/leucine zipper protein Mlx in DNA binding and glucose regulated transcription. Ma L, Sham YY, Walters KJ, Towle HC. Nucleic Acids Research, 35(1): 35-44 (2007). Abstract

  23. Amiodarone analog dependent effects on CYP2C9 mediated metabolism and kinetic profiles. Kumar V, Locuson CW, Sham Y, Tracy TS. Drug Metabolism and Disposition, 34(10): 1688-96 (2006). Abstract

  24. Homology modeling and molecular dynamic simulation of mu opioid receptor in a membrane aqueous system. Zhang Y, Sham YY, Rajamani R, Gao J, Portoghese PS. ChemBioChem, 6(5): 853-59 (2005). Abstract

  25. Platelet factor 4 and interleukin-8 CXC chemokine heterodimer formation modulates function at the quaternary structural level. Nesmelova IV, Sham Y, Dudek AZ, Slungaard A, Mayo KH. Journal of Biological Chemistry, 280(6): 4948-58 (2005). Abstract

  26. Blue Matter, An application framework for molecular simulation on Blue Gene. Fitch BG, Germain RS, Mendell M, Pitera J, Pitman M, Rayshubskiy A, Sham Y, Suits F, Swope W, Ward JJ C, Zhestkov Y, Zhou R, Journal of Parallel and Distributed Computing, 63(7): 759-73 (2003). Abstract

  27. Thermal unfolding molecular dynamic simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway. Sham YY, Ma B, Tsai CJ, Nussinov R. Proteins: Structure, Function, and Bioinformatics, 46(3): 308-20 (2002). Abstract

  28. Critical building blocks in proteins: A common theme on folding and function, Kumar S, Barzilai A, Haspel N, Sham YY, Tsai CJ, Wolfson-HJ and Nussinov R. Recent research Developments in: Protein Folding, Stability and Design. Research Signpost, Trivandrum, India. 207-217 (2002).

  29. A hierarchical, building blocks based computational method for protein structure prediction. Tsai C J, Ma B, Sham YY, Kumar S, Wolfson H, Nussinov R. IBM Journal of Research and Development, 45(3): 513-23 (2001).  Abstract

  30. Case study: An environment for understanding protein simulations using game graphics, Gresh D, Suits F, Sham YY. Proceedings of IEEE Visualization, 445-448 (2001). Abstract

  31. Structured disorder and conformational selection. Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R. Proteins: Structure, Function, and Bioinformatics, 44(4): 418-27 (2001). Abstract

  32. Blue Gene: A vision for protein science using a petaflop supercomputer. Allen F, Almasi G, Andreoni W, Beece D, Berne B J, Bright T, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, Fitch B, Fleischer B, Georgious C J, Germain R, Giampapa M, Gresh D, Gupta M, Haring R, Ho H, Horchschild 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. IBM Systems Journal, 40(2): 310-27 (2001). Abstract

  33. Protein folding and function: The N terminal fragment in adenylate kinase. Kumar S, Sham YY, Tsai CJ, Nussinov R. Biophysical Journal, 80(5): 2439-54 (2001). Abstract

  34. Molecular dynamic simulation of Escherichia coli dihydrofolate reductase and its protein fragments: Relative stability of protein fragments in experiment and simulations. Sham YY, Ma B, Tsai CJ, Nussinov R. Protein Science, 10(1): 135-48 (2001). (Cover Article) Abstract

  35. How important are entropic contributions to enzyme catalysis? Villà J, Strajbl M, Glennon TM, Sham YY, Chu ZT, Warshel A. Proceedings of the National Academy of Sciences, 97(22): 11899-904 (2000). Abstract

  36. Examining methods for calculations of binding free energies: LRA, LIE, PDLD LRA and PDLD/S LRA calculations of ligand binding to HIV protease. Sham YY, Tao H, Chu Z T and Warshel A. Proteins: Structure, Function, and Bioinformatics, 39(4): 393-407 (2000). Abstract

  37. Calculations of activation entropies of chemical reactions in solution. Strajbl S, Sham YY, Villà J, Chu ZT, Warshel A. Journal of Physical Chemistry B 2000, 104(18): 4578-84 (2000). Abstract

  38. Simulating proton translocation in proteins: Probing the proton transfer pathways in the Rhodobacter sphaeroides Reaction Center. Sham YY, Muegge I, Warshel A. Protein: Structure, Function, and Bioinformatics, 36(4): 484-500 (1999). Abstract

  39. The effect of protein relaxation on charge-charge interactions and dielectric constants in proteins. Sham YY, Muegge I, Warshel A. Biophysical Journal 1998, 74(4): 1744-53 (1998). Abstract

  40. The surface constraint all atom model provides size independent results in calculations of hydration free energies. Sham YY, Warshel A. Journal of Chemical Physics 1998, 109(18): 7940-44 (1998). Abstract

  41. Consistent calculations of pKa's of ionizable residues in proteins: semi microscopic and microscopic approaches. Sham YY, Chu ZT, Warshel A. Journal of Physical Chemistry B, 101(22): 4458-72 (1997).  Abstract

  42. Temperature dependent near UV molar absorptivities of several small aldehydes in aqueous solution.  Sham YY, Joens JA. Spectrochimica Acta A, 51(2): 247-51 (1995). Abstract

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