Brent A Gregersen, Xabier Lopez, Darrin M York. J Am Chem Soc 2004
Times Cited: 46
Times Cited: 46
Times Cited
Times Co-cited
Similarity
Hybrid QM/MM study of thio effects in transphosphorylation reactions.
Brent A Gregersen, Xabier Lopez, Darrin M York. J Am Chem Soc 2003
Brent A Gregersen, Xabier Lopez, Darrin M York. J Am Chem Soc 2003
54
The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution.
Kevin Range, Matthew J McGrath, Xabier Lopez, Darrin M York. J Am Chem Soc 2004
Kevin Range, Matthew J McGrath, Xabier Lopez, Darrin M York. J Am Chem Soc 2004
39
Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis.
Carlos Silva López, Olalla Nieto Faza, Brent A Gregersen, Xabier Lopez, Angel R de Lera, Darrin M York. Chemphyschem 2004
Carlos Silva López, Olalla Nieto Faza, Brent A Gregersen, Xabier Lopez, Angel R de Lera, Darrin M York. Chemphyschem 2004
53
How enzymes work: analysis by modern rate theory and computer simulations.
Mireia Garcia-Viloca, Jiali Gao, Martin Karplus, Donald G Truhlar. Science 2004
Mireia Garcia-Viloca, Jiali Gao, Martin Karplus, Donald G Truhlar. Science 2004
32
Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases.
Mikko Oivanen, Satu Kuusela, Harri Lönnberg. Chem Rev 1998
Mikko Oivanen, Satu Kuusela, Harri Lönnberg. Chem Rev 1998
32
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
A Warshel, M Levitt. J Mol Biol 1976
A Warshel, M Levitt. J Mol Biol 1976
32
Isotope effects in the study of phosphoryl and sulfuryl transfer reactions.
Alvan C Hengge. Acc Chem Res 2002
Alvan C Hengge. Acc Chem Res 2002
28
Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis.
Xabier Lopez, Michael Schaefer, Annick Dejaegere, Martin Karplus. J Am Chem Soc 2002
Xabier Lopez, Michael Schaefer, Annick Dejaegere, Martin Karplus. J Am Chem Soc 2002
28
Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis.
Carlos Silva López, Olalla Nieto Faza, Angel R de Lera, Darrin M York. Chemistry 2005
Carlos Silva López, Olalla Nieto Faza, Angel R de Lera, Darrin M York. Chemistry 2005
28
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.
Lee, Yang, Parr. Phys Rev B Condens Matter 1988
Lee, Yang, Parr. Phys Rev B Condens Matter 1988
26
Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory.
Yun Liu, Xabier Lopez, Darrin M York. Chem Commun (Camb) 2005
Yun Liu, Xabier Lopez, Darrin M York. Chem Commun (Camb) 2005
60
Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification.
Yun Liu, Brent A Gregersen, Xabier Lopez, Darrin M York. J Phys Chem B 2005
Yun Liu, Brent A Gregersen, Xabier Lopez, Darrin M York. J Phys Chem B 2005
36
Density-functional exchange-energy approximation with correct asymptotic behavior.
Becke. Phys Rev A Gen Phys 1988
Becke. Phys Rev A Gen Phys 1988
21
Solvent effects on the reaction coordinate of the hydrolysis of phosphates and sulfates: application of Hammond and anti-Hammond postulates to understand hydrolysis in solution.
X Lopez, A Dejaegere, M Karplus. J Am Chem Soc 2001
X Lopez, A Dejaegere, M Karplus. J Am Chem Soc 2001
34
Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom.
D Herschlag, J A Piccirilli, T R Cech. Biochemistry 1991
D Herschlag, J A Piccirilli, T R Cech. Biochemistry 1991
21
Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes.
Evelyn Mayaan, Kevin Range, Darrin M York. J Biol Inorg Chem 2004
Evelyn Mayaan, Kevin Range, Darrin M York. J Biol Inorg Chem 2004
30
Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions.
Dingguo Xu, Hua Guo, Yun Liu, Darrin M York. J Phys Chem B 2005
Dingguo Xu, Hua Guo, Yun Liu, Darrin M York. J Phys Chem B 2005
61
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.
Kwangho Nam, Jiali Gao, Darrin M York. J Chem Theory Comput 2005
Kwangho Nam, Jiali Gao, Darrin M York. J Chem Theory Comput 2005
17
Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
W G Scott, J B Murray, J R Arnold, B L Stoddard, A Klug. Science 1996
W G Scott, J B Murray, J R Arnold, B L Stoddard, A Klug. Science 1996
17
Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory.
Yun Liu, Brent A Gregersen, Alvan Hengge, Darrin M York. Biochemistry 2006
Yun Liu, Brent A Gregersen, Alvan Hengge, Darrin M York. Biochemistry 2006
20
Comparisons of phosphorothioate with phosphate transfer reactions for a monoester, diester, and triester: isotope effect studies.
Irina E Catrina, Alvan C Hengge. J Am Chem Soc 2003
Irina E Catrina, Alvan C Hengge. J Am Chem Soc 2003
19
Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme.
W G Scott. Q Rev Biophys 1999
W G Scott. Q Rev Biophys 1999
17
Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?
J Aqvist, K Kolmodin, J Florian, A Warshel. Chem Biol 1999
J Aqvist, K Kolmodin, J Florian, A Warshel. Chem Biol 1999
15
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.
Christopher J. Cramer, Donald G. Truhlar. Chem Rev 1999
Christopher J. Cramer, Donald G. Truhlar. Chem Rev 1999
15
Computer simulations of enzyme catalysis: methods, progress, and insights.
Arieh Warshel. Annu Rev Biophys Biomol Struct 2003
Arieh Warshel. Annu Rev Biophys Biomol Struct 2003
15
Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution.
Brent A Gregersen, Jana Khandogin, Walter Thiel, Darrin M York. J Phys Chem B 2005
Brent A Gregersen, Jana Khandogin, Walter Thiel, Darrin M York. J Phys Chem B 2005
50
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods.
Jana Khandogin, Darrin M York. Proteins 2004
Jana Khandogin, Darrin M York. Proteins 2004
18
The hairpin ribozyme: structure, assembly and catalysis.
N G Walter, J M Burke. Curr Opin Chem Biol 1998
N G Walter, J M Burke. Curr Opin Chem Biol 1998
15
Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms.
Kwangho Nam, Qiang Cui, Jiali Gao, Darrin M York. J Chem Theory Comput 2007
Kwangho Nam, Qiang Cui, Jiali Gao, Darrin M York. J Chem Theory Comput 2007
15
Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems.
Xabier Lopez, Annick Dejaegere, Fabrice Leclerc, Darrin M York, Martin Karplus. J Phys Chem B 2006
Xabier Lopez, Annick Dejaegere, Fabrice Leclerc, Darrin M York, Martin Karplus. J Phys Chem B 2006
15
The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA.
De-Min Zhou, Kazunari Taira. Chem Rev 1998
De-Min Zhou, Kazunari Taira. Chem Rev 1998
13
Estimating pKa values for pentaoxyphosphoranes.
J E Davies, N L Doltsinis, A J Kirby, C D Roussev, M Sprik. J Am Chem Soc 2002
J E Davies, N L Doltsinis, A J Kirby, C D Roussev, M Sprik. J Am Chem Soc 2002
13
Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods.
Jana Khandogin, Karin Musier-Forsyth, Darrin M York. J Mol Biol 2003
Jana Khandogin, Karin Musier-Forsyth, Darrin M York. J Mol Biol 2003
22
Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.
Jana Khandogin, Brent A Gregersen, Walter Thiel, Darrin M York. J Phys Chem B 2005
Jana Khandogin, Brent A Gregersen, Walter Thiel, Darrin M York. J Phys Chem B 2005
28
Transition state stabilization by a catalytic RNA.
Peter B Rupert, Archna P Massey, Snorri Th Sigurdsson, Adrian R Ferré-D'Amaré. Science 2002
Peter B Rupert, Archna P Massey, Snorri Th Sigurdsson, Adrian R Ferré-D'Amaré. Science 2002
13
Thiolysis and alcoholysis of phosphate tri- and monoesters with alkyl and aryl leaving groups. An ab initio study in the gas phase.
Guilherme Menegon Arantes, Hernan Chaimovich. J Phys Chem A 2005
Guilherme Menegon Arantes, Hernan Chaimovich. J Phys Chem A 2005
26
Ribozyme speed limits.
Gail Mitchell Emilsson, Shingo Nakamura, Adam Roth, Ronald R Breaker. RNA 2003
Gail Mitchell Emilsson, Shingo Nakamura, Adam Roth, Ronald R Breaker. RNA 2003
13
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.
Demian Riccardi, Patricia Schaefer, Yang Yang, Haibo Yu, Nilanjan Ghosh, Xavier Prat-Resina, Peter König, Guohui Li, Dingguo Xu, Hua Guo,[...]. J Phys Chem B 2006
Demian Riccardi, Patricia Schaefer, Yang Yang, Haibo Yu, Nilanjan Ghosh, Xavier Prat-Resina, Peter König, Guohui Li, Dingguo Xu, Hua Guo,[...]. J Phys Chem B 2006
13
QCRNA 1.0: a database of quantum calculations for RNA catalysis.
Timothy J Giese, Brent A Gregersen, Yun Liu, Kwangho Nam, Evelyn Mayaan, Adam Moser, Kevin Range, Olalla Nieto Faza, Carlos Silva Lopez, Angel Rodriguez de Lera,[...]. J Mol Graph Model 2006
Timothy J Giese, Brent A Gregersen, Yun Liu, Kwangho Nam, Evelyn Mayaan, Adam Moser, Kevin Range, Olalla Nieto Faza, Carlos Silva Lopez, Angel Rodriguez de Lera,[...]. J Mol Graph Model 2006
26
Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
10
10
Quantum mechanical calculations on biological systems.
R A Friesner, M D Beachy. Curr Opin Struct Biol 1998
R A Friesner, M D Beachy. Curr Opin Struct Biol 1998
10
General acid catalysis by the hepatitis delta virus ribozyme.
Subha R Das, Joseph A Piccirilli. Nat Chem Biol 2005
Subha R Das, Joseph A Piccirilli. Nat Chem Biol 2005
10
Importance of van der Waals Interactions in QM/MM Simulations.
Demian Riccardi, Guohui Li, Qiang Cui. J Phys Chem B 2004
Demian Riccardi, Guohui Li, Qiang Cui. J Phys Chem B 2004
10
Synthesis and Properties of Diuridine Phosphate Analogues Containing Thio and Amino Modifications.
James B. Thomson, Bhisma K. Patel, Victor Jiménez, Klaus Eckart, Fritz Eckstein. J Org Chem 1996
James B. Thomson, Bhisma K. Patel, Victor Jiménez, Klaus Eckart, Fritz Eckstein. J Org Chem 1996
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A general two-metal-ion mechanism for catalytic RNA.
T A Steitz, J A Steitz. Proc Natl Acad Sci U S A 1993
T A Steitz, J A Steitz. Proc Natl Acad Sci U S A 1993
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All-atom empirical potential for molecular modeling and dynamics studies of proteins.
A D MacKerell, D Bashford, M Bellott, R L Dunbrack, J D Evanseck, M J Field, S Fischer, J Gao, H Guo, S Ha,[...]. J Phys Chem B 1998
A D MacKerell, D Bashford, M Bellott, R L Dunbrack, J D Evanseck, M J Field, S Fischer, J Gao, H Guo, S Ha,[...]. J Phys Chem B 1998
10
8
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.