A citation-based method for searching scientific literature

Brent A Gregersen, Xabier Lopez, Darrin M York. J Am Chem Soc 2004
Times Cited: 46







List of co-cited articles
359 articles co-cited >1



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
37
54


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
30
53

How enzymes work: analysis by modern rate theory and computer simulations.
Mireia Garcia-Viloca, Jiali Gao, Martin Karplus, Donald G Truhlar. Science 2004
674
32




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
79
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
46
28










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
357
17





Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.
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
339
15



The hairpin ribozyme: structure, assembly and catalysis.
N G Walter, J M Burke. Curr Opin Chem Biol 1998
99
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
54
15


Estimating pKa values for pentaoxyphosphoranes.
J E Davies, N L Doltsinis, A J Kirby, C D Roussev, M Sprik. J Am Chem Soc 2002
81
13


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
21
28

Why nature chose phosphates.
F H Westheimer. Science 1987
721
13


Transition state stabilization by a catalytic RNA.
Peter B Rupert, Archna P Massey, Snorri Th Sigurdsson, Adrian R Ferré-D'Amaré. Science 2002
219
13


Ribozyme speed limits.
Gail Mitchell Emilsson, Shingo Nakamura, Adam Roth, Ronald R Breaker. RNA 2003
155
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
218
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
23
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
10

Escaping free-energy minima.
Alessandro Laio, Michele Parrinello. Proc Natl Acad Sci U S A 2002
10

Quantum mechanical calculations on biological systems.
R A Friesner, M D Beachy. Curr Opin Struct Biol 1998
63
10

General acid catalysis by the hepatitis delta virus ribozyme.
Subha R Das, Joseph A Piccirilli. Nat Chem Biol 2005
177
10

Importance of van der Waals Interactions in QM/MM Simulations.
Demian Riccardi, Guohui Li, Qiang Cui. J Phys Chem B 2004
71
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
39
12

A general two-metal-ion mechanism for catalytic RNA.
T A Steitz, J A Steitz. Proc Natl Acad Sci U S A 1993
903
10

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
10

Ribozyme structures and mechanisms.
E A Doherty, J A Doudna. Annu Rev Biophys Biomol Struct 2001
132
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.