(Q34330910)

1 August 2017

1 reference

title

Molecular modeling of drug-DNA complexes: an update (English)

1 reference

1 August 2017

Trent JO

1

1 reference

PubMed ID

11494855

1 August 2017

language of work or name

English

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publication date

1 January 2001

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1 August 2017

Methods in Enzymology

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1 August 2017

340

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1 August 2017

290-326

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Targeting DNA with triplexes

1 August 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Triplex-directed modification of genes and gene activity

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Inhibition of transcription of the human c-myc protooncogene by intermolecular triplex

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Triplex DNA: fundamentals, advances, and potential applications for gene therapy

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Antisense therapeutics: is it as simple as complementary base recognition?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Progress in antisense technology: the end of the beginning

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure determination and binding kinetics of a DNA aptamer-argininamide complex

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Effect of loop sequence and size on DNA aptamer stability

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A DNA aptamer that binds adenosine and ATP.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Oligonucleotides as research, diagnostic, and therapeutic agents

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Antiproliferative activity of G-rich oligonucleotides correlates with protein binding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular recognition of cAMP by an RNA aptamer.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Sequence-specific DNA recognition by polyamides

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure-based design of a new bisintercalating anthracycline antibiotic

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Bisanthracycline WP631 inhibits basal and Sp1-activated transcription initiation in vitro.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A gene expression database for the molecular pharmacology of cancer

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Nucleic acids: theory and computer simulation, Y2K.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics simulation of nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Mixed QM/MM molecular electrostatic potentials.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics simulations of biomolecules: long-range electrostatic effects

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Semianalytical treatment of solvation for molecular mechanics and dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Dielectric response of triplex DNA in ionic solution from simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular Dynamics Simulations of PNA·DNA and PNA·RNA Duplexes in Aqueous Solution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The B-DNA dodecamer at high resolution reveals a spine of water on sodium

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structural equilibrium of DNA represented with different force fields

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC)2: implications for recognition by minor groove binding drugs.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics simulations of DNA in solutions with different counter-ions.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A unified theory of the B-Z transition of DNA in high and low concentrations of multivalent ions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2Complex determined by NMR and molecular dynamics simulations in solution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

DNA minor groove recognition by a tetrahydropyrimidinium analogue of hoechst 33258: NMR and molecular dynamics studies of the complex with d(GGTAATTACC)2.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular recognition between a new pentacyclic acridinium salt and DNA sequences investigated by optical spectroscopic techniques, proton nuclear magnetic resonance spectroscopy, and molecular modeling

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular Dynamics Simulations in Aqueous Solution of Triple Helices Containing d(G·C·C) Trios

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Solvent effects on model d(CG.G)7 and d(TA.T)7 DNA triple helices

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Stabilization of DNA triple helices by a series of mono- and disubstituted amidoanthraquinones

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Determinants of DNA quadruplex structural type: sequence and potassium binding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Inhibition of human telomerase by a G-quadruplex-interactive compound

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Human telomerase inhibition by regioisomeric disubstituted amidoanthracene-9,10-diones

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

General atomic and molecular electronic structure system

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure of a triple helical DNA with a triplex-duplex junction

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Symmetry and molecular structure of a DNA triple helix: d(T)n.d(A)n.d(T)n.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Symmetry and structure of RNA and DNA triple helices.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Structure of d(T)n.d(A)n.d(T)n: the DNA triple helix has B-form geometry with C2'-endo sugar pucker

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Identification of preferred distamycin-DNA binding sites by the combinatorial method REPSA

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Definitions and nomenclature of nucleic acid structure components

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Overview of nucleic acid analysis programs

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

VMD: visual molecular dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Classical electrostatics in biology and chemistry

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular dynamics of structural transitions and intercalation in DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Left-handed intercalated DNA double helix: rendezvous of ethidium and actinomycin D in the Z-helical conformation space

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Nuclear localization and DNA binding of the transforming gene product of avian myelocytomatosis virus

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The G-C specific DNA binding drug, mithramycin, selectively inhibits transcription of the C-MYC and C-HA-RAS genes in regenerating liver

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The c-myc promoter binding protein (MBP-1) and TBP bind simultaneously in the minor groove of the c-myc P2 promoter

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Influence of GC and AT specific DNA minor groove binding drugs on intermolecular triplex formation in the human c-Ki-ras promoter

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Triplex stability of oligodeoxynucleotides containing substituted quinazoline-2,4-(1H,3H)-dione

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Potassium-resistant triple helix formation and improved intracellular gene targeting by oligodeoxyribonucleotides containing 7-deazaxanthine

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The contribution of cytosine protonation to the stability of parallel DNA triple helices

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Solution Structure of an Intramolecular Pyrimidine−Purine−Pyrimidine Triplex Containing an RNA Third Strand

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

NMR structural studies of intramolecular (Y+)n.(R+)n(Y-)nDNA triplexes in solution: imino and amino proton and nitrogen markers of G.TA base triple formation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Hydration sites in purine.purine.pyrimidine and pyrimidine.purine.pyrimidine DNA triplexes in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

NMR-Based model of a telomerase-inhibiting compound bound to G-quadruplex DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Determination of the number and location of the manganese binding sites of DNA quadruplexes in solution by EPR and NMR in the presence and absence of thrombin

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The high-resolution crystal structure of a parallel-stranded guanine tetraplex

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

Molecular modelling of the interactions of tetra-(4-N-methylpyridyl) porphin with TA and CG sites on DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

A smooth particle mesh Ewald method

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2801%2940428-9

7 January 2021

10.1016/S0076-6879(01)40428-9

Identifiers

DOI

1 reference

1 August 2017

1 reference

PubMed ID

11494855