Fast approximate methods for calculating nucleic acid base pair interaction energies

Edward C. Sherer; Darrin M. York; Christopher J. Cramer

doi:10.1002/jcc.10150

Fast approximate methods for calculating nucleic acid base pair interaction energies

Journal of Computational Chemistry ◽

10.1002/jcc.10150 ◽

2003 ◽

Vol 24 (1) ◽

pp. 57-67 ◽

Cited By ~ 24

Author(s):

Edward C. Sherer ◽

Darrin M. York ◽

Christopher J. Cramer

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Pair Interaction ◽

Interaction Energies ◽

Acid Base ◽

Approximate Methods ◽

Nucleic Acid Base

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A standard reference frame for the description of nucleic acid base-pair geometry 1 1Edited by P. E. Wright 2 2This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.

Journal of Molecular Biology ◽

10.1006/jmbi.2001.4987 ◽

2001 ◽

Vol 313 (1) ◽

pp. 229-237 ◽

Cited By ~ 371

Author(s):

Wilma K Olson ◽

Manju Bansal ◽

Stephen K Burley ◽

Richard E Dickerson ◽

Mark Gerstein ◽

...

Keyword(s):

Nucleic Acid ◽

Reference Frame ◽

Base Pair ◽

Joint Commission ◽

Acid Base ◽

Nomenclature Committee ◽

Biochemical Nomenclature ◽

Nucleic Acid Base

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ChemInform Abstract: Synthesis and X-Ray Crystal Structure of a Novel Tetrathiafulvalene Dimethyl(2,4-dioxo(1H,3H)pyrimido)tetrathiafulvalene, Able to Form Intermolecular Hydrogen Bonds of Nucleic Acid Base-Pair Type.

ChemInform ◽

10.1002/chin.199527161 ◽

2010 ◽

Vol 26 (27) ◽

pp. no-no

Author(s):

O. NEILANDS ◽

S. BELYAKOV ◽

V. TILIKA ◽

A. EDZINA

Keyword(s):

Crystal Structure ◽

Nucleic Acid ◽

Hydrogen Bonds ◽

Base Pair ◽

Pair Type ◽

Acid Base ◽

Intermolecular Hydrogen Bonds ◽

X Ray ◽

Nucleic Acid Base

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Flexibly capped β-cyclodextrins by the hydrogen-bonded nucleic acid base pair. The pH-control of binding ability by an on-off-switched capping

Tetrahedron Letters ◽

10.1016/s0040-4039(00)98325-4 ◽

1985 ◽

Vol 26 (14) ◽

pp. 1735-1738 ◽

Cited By ~ 7

Author(s):

Katuyuki Nagai ◽

Shigeo Ukal ◽

Kenji Hayakawa ◽

Ken Kanematsu

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Ph Control ◽

Acid Base ◽

Binding Ability ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Nucleobase difunctionalized .beta.-cyclodextrins. Preparation and spectral observation of base stacking and the hydrogen-bonded nucleic acid base pair

The Journal of Organic Chemistry ◽

10.1021/jo00371a003 ◽

1986 ◽

Vol 51 (21) ◽

pp. 3931-3939 ◽

Cited By ~ 8

Author(s):

Katsuyuki Nagai ◽

Kenji Hayakawa ◽

Shigeo Ukai ◽

Ken Kanematsu

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Spectral Observation ◽

Base Stacking ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Møller–Plesset perturbation theory

Physical Chemistry Chemical Physics ◽

10.1039/b718691f ◽

2008 ◽

Vol 10 (19) ◽

pp. 2785 ◽

Cited By ~ 40

Author(s):

J. Grant Hill ◽

James A. Platts

Keyword(s):

Perturbation Theory ◽

Nucleic Acid ◽

Base Pair ◽

Second Order ◽

Spin Component ◽

Stacking Interactions ◽

Acid Base ◽

Nucleic Acid Base ◽

Moller Plesset ◽

Plesset Perturbation Theory

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Biological agent identification by nucleic acid base-pair analysis using surface-enhanced Raman spectroscopy

10.1117/12.336858 ◽

1999 ◽

Author(s):

Stuart Farquharson ◽

Wayne W. Smith ◽

Susan Elliott ◽

Jay F. Sperry

Keyword(s):

Raman Spectroscopy ◽

Nucleic Acid ◽

Base Pair ◽

Surface Enhanced Raman Spectroscopy ◽

Biological Agent ◽

Acid Base ◽

Surface Enhanced ◽

Nucleic Acid Base ◽

Surface Enhanced Raman ◽

Pair Analysis

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Ab Initio Interaction Energies of Hydrogen-Bonded Amino Acid Side Chain−Nucleic Acid Base Interactions

Journal of the American Chemical Society ◽

10.1021/ja037264g ◽

2004 ◽

Vol 126 (2) ◽

pp. 434-435 ◽

Cited By ~ 40

Author(s):

Alan C. Cheng ◽

Alan D. Frankel

Keyword(s):

Amino Acid ◽

Nucleic Acid ◽

Ab Initio ◽

Side Chain ◽

Amino Acid Side Chain ◽

Interaction Energies ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Interaction of Ia and IIa group cations with the guanine site in cytosine-guanine nucleic acid base pair: an ab initio Hartree Fock study in the absence of basis set superposition error

Computers & Chemistry ◽

10.1016/s0097-8485(99)00074-1 ◽

2000 ◽

Vol 24 (3-4) ◽

pp. 341-349 ◽

Cited By ~ 7

Author(s):

Antonino Famulari ◽

Federico Moroni ◽

Maurizio Sironi ◽

Mario Raimondi

Keyword(s):

Nucleic Acid ◽

Ab Initio ◽

Base Pair ◽

Basis Set ◽

Acid Base ◽

Basis Set Superposition Error ◽

Hartree Fock ◽

Nucleic Acid Base

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ChemInform Abstract: FLEXIBLY CAPPED β-CYCLODEXTRINS BY THE HYDROGEN-BONDED NUCLEIC ACID BASE PAIR. THE PH-CONTROL OF BINDING ABILITY BY AN ON-OFF-SWITCHED CAPPING

Chemischer Informationsdienst ◽

10.1002/chin.198529361 ◽

1985 ◽

Vol 16 (29) ◽

Author(s):

K. NAGAI ◽

S. UKAI ◽

K. HAYAKAWA ◽

K. KANEMATSU

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Ph Control ◽

Acid Base ◽

Binding Ability ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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DFT Investigation of the Interaction of Gold Nanoclusters with Nucleic Acid Base Guanine and the Watson−Crick Guanine-Cytosine Base Pair

The Journal of Physical Chemistry C ◽

10.1021/jp808622y ◽

2009 ◽

Vol 113 (10) ◽

pp. 3960-3966 ◽

Cited By ~ 35

Author(s):

Manoj K. Shukla ◽

Madan Dubey ◽

Eugene Zakar ◽

Jerzy Leszczynski

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Gold Nanoclusters ◽

Acid Base ◽

Nucleic Acid Base

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