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  1. 1.   Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis
  2. Dharavath,Sudhaker; Shaw,Gary; Ji,Xinhua
  3. RNA Biology. 2022, Jan; 19(1): 908-915.
  1. 2.   The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation
  2. Lyonnais, Sébastien; Sadiq, S Kashif; Lorca-Oró, Cristina; Dufau, Laure; Nieto-Marquez, Sara; Escribà, Tuixent; Gabrielli, Natalia; Tan, Xiao; Ouizougun-Oubari, Mohamed; Okoronkwo, Josephine; Reboud-Ravaux, Michèle; Gatell, José Maria; Marquet, Roland; Paillart, Jean-Christophe; Meyerhans, Andreas; Tisné, Carine; Gorelick,Robert; Mirambeau, Gilles
  3. Viruses. 2021, Nov 19; 13(11):
  1. 3.   Measuring RNA-Ligand Interactions with Microscale Thermophoresis
  2. Moon, Michelle H.; Hilimire, Thomas A.; Sanders, Allix M.; Schneekloth, Jay
  3. BIOCHEMISTRY. 2018, Aug 7; 57(31): 4638-4643.
  1. 4.   The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 angstrom Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations
  2. Sharma, S.; Bhaumik, P.; Schmitz, W.; Venkatesan, R.; Hiltunen, J. K.; Conzelmann, E.; Juffer, A. H.; Wierenga, R. K.
  3. Journal of Physical Chemistry B. 2012, Mar; 116(11): 3619-3629.
  1. 5.   DENDRONIZED BI-2-QUINOLINE LIGANDS AND THEIR METAL COMPLEXES: DENDRON SYNTHESIS AND METALLOASSEMBLY
  2. Patri, A.; Moorefield, C. N.; Newkome, G. R.
  3. Heterocycles. 2012, Jan; 84(2): 1023-1032.
  1. 6.   Ionic Liquids: Neoteric Solvents for Nucleoside Chemistry
  2. Kumar, V.; Parmar, V. S.; Malhotra, S. V.
  3. Current Organic Synthesis. 2011, Dec; 8(6): 777-786.
  1. 7.   Interaction of RNA Polymerase II Fork Loop 2 with Downstream Non-template DNA Regulates Transcription Elongation
  2. Kireeva, M. L.; Domecq, C.; Coulombe, B.; Burton, Z. F.; Kashlev, M.
  3. Journal of Biological Chemistry. 2011, Sep; 286(35): 30898-30910.
  1. 8.   Role of Protein Conformational Dynamics in the Catalysis by 6-Hydroxymethyl-7, 8-Dihydropterin Pyrophosphokinase
  2. Yan, H. G.; Ji, X. H.
  3. Protein and Peptide Letters. 2011, Apr; 18(4): 328-335.
  1. 9.   Allostery and population shift in drug discovery
  2. Kar, G.; Keskin, O.; Gursoy, A.; Nussinov, R.
  3. Current Opinion in Pharmacology. 2010, Dec; 10(6): 715-722.
  1. 10.   Structural modifications of nucleosides in ionic liquids
  2. Kumar, V.; Parmar, V. S.; Malhotra, S. V.
  3. Biochimie. 2010, Sep; 92(9): 1260-1265.
  1. 11.   The role of dynamic conformational ensembles in biomolecular recognition
  2. Boehr, D. D.; Nussinov, R.; Wright, P. E.
  3. Nature Chemical Biology. 2009 5(11): 789-796.
  1. 12.   Amplification of signaling via cellular allosteric relay and protein disorder
  2. Ma, B. Y.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2009 106(17): 6887-6888.
  1. 13.   Regioselective epoxide ring-opening using boron trifluoride diethyl etherate: DFT study of an alternative mechanism to explain the formation of syn-fluorohydrins
  2. Mendez, P. S.; Cachau, R. E.; Seoane, G.; Ventura, O. N.
  3. Journal of Molecular Structure-theochem. 2009 904(1-3): 21-27.
  1. 14.   A stepwise model for double-stranded RNA processing by ribonuclease III
  2. Gan, J.; Shaw, G.; Tropea, J. E.; Waugh, D. S.; Court, D. L.; Ji, X.
  3. Molecular Microbiology. 2008 67(1): 143-154.
  1. 15.   FeCl3-catalyzed Pechmann synthesis of coumarins in ionic liquids
  2. Kumar, V.; Tomar, S.; Patel, R.; Yousaf, A.; Parmar, V. S.; Malhotra, S. V.
  3. Synthetic Communications. 2008 38(15): 2646-2654.
  1. 16.   Ligand binding and circular permutation modify residue interaction network in DHFR
  2. Hu, Z. J.; Bowen, D.; Southerl, W. M.; del Sol, A.; Pan, Y. P.; Nussinov, R.; Ma, B. Y.
  3. Plos Computational Biology. 2007, Jun; 3(6): 1097-1107.
  1. 17.   Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling
  2. Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K.; Martinez, H. M.; Nemukhin, A. V.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2007, Apr; 104(17): 7057-7061.
  1. 18.   The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As
  2. Xu, Q.; Guo, H. B.; Wlodawer, A.; Nakayama, T.; Guo, H.
  3. Biochemistry. 2007, Mar; 46(12): 3784-3792.
  1. 19.   The importance of dynamics in substrate-assisted catalysis and specificity
  2. Xu, Q.; Guo, H.; Wlodawer, A.; Guo, H.
  3. Journal of the American Chemical Society. 2006, MAY 10; 128(18): 5994-5995.
  1. 20.   Examining Ty3 polypurine tract structure and function by nucleoside analog interference
  2. Dash, C.; Marino, J. P.; Le Grice, S. F. J.
  3. Journal of Biological Chemistry. 2006, FEB 3; 281(5): 2773-2783.
  1. 21.   Effect of hydrophobic structure on the catalysis of nitric oxide release from zwitterionic diazeniumdiolates in surfactant and liposome media
  2. Dinh, B.; Dove, K.; Jappar, D.; Hrabie, J. A.; Davies, K. M.
  3. Nitric Oxide-Biology and Chemistry. 2005, NOV; 13(3): 204-209.
  1. 22.   Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies
  2. Li, Y.; Blaszczyk, J.; Wu, Y.; Shi, G. B.; Ji, X. H.; Yan, H. G.
  3. Biochemistry. 2005, JUN 21; 44(24): 8590-8599.
  1. 23.   Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase
  2. Bibillo, A.; Lener, D.; Klarmann, G. J.; Le Grice, S. F. J.
  3. Nucleic Acids Research. 2005 33(1): 171-181.
  1. 24.   Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
  2. Blaszczyk, J.; Li, Y.; Wu, Y.; Shi, G. B.; Ji, X. H.; Yan, H. G.
  3. Biochemistry. 2004 43(6): 1469-1477.
  1. 25.   The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site
  2. Botos, I.; Melnikov, E. E.; Cherry, S.; Tropea, J. E.; Khalatova, A. G.; Rasulova, F.; Dauter, Z.; Maurizi, M. R.; Rotanova, T. V.; Wlodawer, A.; Gustchina, A.
  3. Journal of Biological Chemistry. 2004 279(9): 8140-8148.
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