A citation-based method for searching scientific literature

Sarah A Woodson. Curr Opin Chem Biol 2005
Times Cited: 247







List of co-cited articles
1230 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Ions and RNA folding.
David E Draper, Dan Grilley, Ana Maria Soto. Annu Rev Biophys Biomol Struct 2005
327
28

A guide to ions and RNA structure.
David E Draper. RNA 2004
393
24

Understanding nucleic acid-ion interactions.
Jan Lipfert, Sebastian Doniach, Rhiju Das, Daniel Herschlag. Annu Rev Biochem 2014
209
22

Metal ions in the structure and function of RNA.
Anna Marie Pyle. J Biol Inorg Chem 2002
241
21




How RNA folds.
I Tinoco, C Bustamante. J Mol Biol 1999
579
16

Charge density of divalent metal cations determines RNA stability.
Eda Koculi, Changbong Hyeon, D Thirumalai, Sarah A Woodson. J Am Chem Soc 2007
113
15

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Alberto Pérez, Iván Marchán, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco. Biophys J 2007
15

RNA helix stability in mixed Na+/Mg2+ solution.
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2007
67
22




Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
T Xia, J SantaLucia, M E Burkard, R Kierzek, S J Schroeder, X Jiao, C Cox, D H Turner. Biochemistry 1998
799
14

Hierarchy and dynamics of RNA folding.
P Brion, E Westhof. Annu Rev Biophys Biomol Struct 1997
402
13


Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Ryan L Hayes, Jeffrey K Noel, Udayan Mohanty, Paul C Whitford, Scott P Hennelly, José N Onuchic, Karissa Y Sanbonmatsu. J Am Chem Soc 2012
58
22

How do metal ions direct ribozyme folding?
Natalia A Denesyuk, D Thirumalai. Nat Chem 2015
52
25


Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions.
Ana Maria Soto, Vinod Misra, David E Draper. Biochemistry 2007
87
13

Cations in charge: magnesium ions in RNA folding and catalysis.
Jessica C Bowman, Timothy K Lenz, Nicholas V Hud, Loren Dean Williams. Curr Opin Struct Biol 2012
115
12

Coarse-grained model for predicting RNA folding thermodynamics.
Natalia A Denesyuk, D Thirumalai. J Phys Chem B 2013
72
16



VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
11

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.
Serdal Kirmizialtin, Suzette A Pabit, Steve P Meisburger, Lois Pollack, Ron Elber. Biophys J 2012
67
16



Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.
Marie Zgarbová, Michal Otyepka, Jiří Sponer, Arnošt Mládek, Pavel Banáš, Thomas E Cheatham, Petr Jurečka. J Chem Theory Comput 2011
507
11

A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu, Zhi-Jie Tan. J Chem Phys 2014
40
27

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids.
Yu Bai, Max Greenfeld, Kevin J Travers, Vincent B Chu, Jan Lipfert, Sebastian Doniach, Daniel Herschlag. J Am Chem Soc 2007
169
10

A compact RNA tertiary structure contains a buried backbone-K+ complex.
Graeme L Conn, Apostolos G Gittis, Eaton E Lattman, Vinod K Misra, David E Draper. J Mol Biol 2002
100
10

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.
Yuan-Yan Wu, Zhong-Liang Zhang, Jin-Si Zhang, Xiao-Long Zhu, Zhi-Jie Tan. Nucleic Acids Res 2015
39
25

Physics-based de novo prediction of RNA 3D structures.
Song Cao, Shi-Jie Chen. J Phys Chem B 2011
88
11

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.
Ryan L Hayes, Jeffrey K Noel, Ana Mandic, Paul C Whitford, Karissa Y Sanbonmatsu, Udayan Mohanty, José N Onuchic. Phys Rev Lett 2015
35
28

RNA 3D structure prediction by using a coarse-grained model and experimental data.
Zhen Xia, David R Bell, Yue Shi, Pengyu Ren. J Phys Chem B 2013
51
19

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Michal J Boniecki, Grzegorz Lach, Wayne K Dawson, Konrad Tomala, Pawel Lukasz, Tomasz Soltysinski, Kristian M Rother, Janusz M Bujnicki. Nucleic Acids Res 2016
146
10

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs.
Alexander Serganov, Yu-Ren Yuan, Olga Pikovskaya, Anna Polonskaia, Lucy Malinina, Anh Tuân Phan, Claudia Hobartner, Ronald Micura, Ronald R Breaker, Dinshaw J Patel. Chem Biol 2004
404
9


Electrostatics of nanosystems: application to microtubules and the ribosome.
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
9


Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.
Dan Grilley, Ana Maria Soto, David E Draper. Proc Natl Acad Sci U S A 2006
84
10

Ion counting from explicit-solvent simulations and 3D-RISM.
George M Giambaşu, Tyler Luchko, Daniel Herschlag, Darrin M York, David A Case. Biophys J 2014
57
15

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.
Huimin Chen, Steve P Meisburger, Suzette A Pabit, Julie L Sutton, Watt W Webb, Lois Pollack. Proc Natl Acad Sci U S A 2012
194
9

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V Demidov, Natalia E Broude, Nikolay V Dokholyan. RNA 2008
186
9

Importance of diffuse metal ion binding to RNA.
Zhi-Jie Tan, Shi-Jie Chen. Met Ions Life Sci 2011
29
31

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.
Olof Allnér, Lennart Nilsson, Alessandra Villa. J Chem Theory Comput 2012
214
9

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
9

Salt dependence of nucleic acid hairpin stability.
Zhi-Jie Tan, Shi-Jie Chen. Biophys J 2008
63
14


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.