Literature DB >> 20012413

Molecular modeling and simulation of G-quadruplexes and quadruplex-ligand complexes.

Shozeb Haider1, Stephen Neidle.   

Abstract

Methods for the molecular modeling and simulation of G-quadruplex structures and their drug/ligand complexes are discussed, and a range of protocols is presented for undertaking a variety of tasks including model-building, ligand docking, dynamics simulation, continuum solvent modeling, energetic calculations, principal component analysis, and quantum chemical computations. The scope and limitations of these approaches are discussed.

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Year:  2010        PMID: 20012413     DOI: 10.1007/978-1-59745-363-9_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  18 in total

1.  Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.

Authors:  Jiří Šponer; Arnošt Mládek; Naďa Špačková; Xiaohui Cang; Thomas E Cheatham; Stefan Grimme
Journal:  J Am Chem Soc       Date:  2013-06-19       Impact factor: 15.419

Review 2.  Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.

Authors:  Jiří Sponer; Xiaohui Cang; Thomas E Cheatham
Journal:  Methods       Date:  2012-04-16       Impact factor: 3.608

3.  G4LDB: a database for discovering and studying G-quadruplex ligands.

Authors:  Qian Li; Jun-Feng Xiang; Qian-Fan Yang; Hong-Xia Sun; Ai-Jiao Guan; Ya-Lin Tang
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

4.  Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions.

Authors:  Iztok Prislan; Jurij Lah; Matija Milanic; Gorazd Vesnaver
Journal:  Nucleic Acids Res       Date:  2010-11-26       Impact factor: 16.971

5.  Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

Authors:  Roman V Reshetnikov; Jiri Sponer; Olga I Rassokhina; Alexei M Kopylov; Philipp O Tsvetkov; Alexander A Makarov; Andrey V Golovin
Journal:  Nucleic Acids Res       Date:  2011-09-05       Impact factor: 16.971

6.  G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch.

Authors:  Ai-Jiao Guan; Meng-Jie Shen; Jun-Feng Xiang; En-Xuan Zhang; Qian Li; Hong-Xia Sun; Li-Xia Wang; Guang-Zhi Xu; Ya-Lin Tang; Li-Jin Xu; Han-Yuan Gong
Journal:  Sci Rep       Date:  2015-05-20       Impact factor: 4.379

7.  Discovery of a structural-element specific G-quadruplex "light-up" probe.

Authors:  Liyun Zhang; Jun Cheng Er; Krishna Kanta Ghosh; Wan Jun Chung; Jaeduk Yoo; Wang Xu; Wei Zhao; Anh Tuân Phan; Young-Tae Chang
Journal:  Sci Rep       Date:  2014-01-20       Impact factor: 4.379

8.  Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands.

Authors:  Michael P O'Hagan; Susanta Haldar; Juan C Morales; Adrian J Mulholland; M Carmen Galan
Journal:  Chem Sci       Date:  2020-11-26       Impact factor: 9.825

9.  An in silico study of the differential effect of oxidation on two biologically relevant G-quadruplexes: possible implications in oncogene expression.

Authors:  William J D Stebbeds; Joseph Lunec; Lee D Larcombe
Journal:  PLoS One       Date:  2012-08-22       Impact factor: 3.240

10.  An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation.

Authors:  Huy T Le; William L Dean; Robert Buscaglia; Jonathan B Chaires; John O Trent
Journal:  J Phys Chem B       Date:  2014-05-08       Impact factor: 2.991

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