(Q24811382)

5 July 2017

title

Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations (English)

1 reference

5 July 2017

1 reference

Remo Rohs

1

1 reference

5 July 2017

Itai Bloch

series ordinal

2

1 reference

5 July 2017

Heinz Sklenar

series ordinal

3

1 reference

5 July 2017

Zippora Shakked

series ordinal

4

1 reference

5 July 2017

language of work or name

English

0 references

publication date

13 December 2005

1 reference

5 July 2017

published in

Nucleic Acids Research

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5 July 2017

volume

33

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5 July 2017

issue

22

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5 July 2017

page(s)

7048-7057

1 reference

The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites

5 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Principles of docking: An overview of search algorithms and a guide to scoring functions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Designed sequence-specific minor groove ligands

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Defining the structure of irregular nucleic acids: conventions and principles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

The phenothiazinium chromophore and the evolution of antimalarial drugs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

On proteins, grids, correlations, and docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Docking macromolecules with flexible segments.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Thermodynamics of drug-DNA interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

DNA-binding of drugs used in medicinal therapies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Cooperativity in drug-DNA recognition: a molecular dynamics study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Molecular modeling of drug-DNA complexes: an update

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

DNA minor-groove recognition by small molecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

FlexE: efficient molecular docking considering protein structure variations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Sequence specific recognition of ligand-DNA complexes studied by NMR.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Dynamical view of the positions of key side chains in protein-protein recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Drug-DNA recognition: energetics and implications for design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Unraveling proteins: a molecular mechanics study

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

28 September 2017

Drug--DNA interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Photochemical interactions of methylene blue and analogues with DNA and other biological substrates.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Complexes of the minor groove of DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

DNA as a target for drug action

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Crystal structures of nucleic acids and their drug complexes

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Monte Carlo docking of oligopeptides to proteins.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Bending in the right direction.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Complementarity of Structure Ensembles in Protein-Protein Binding

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Predicting interactions of winged-helix transcription factors with DNA.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

ICM-DISCO docking by global energy optimization with fully flexible side-chains

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Methylene blue binding to DNA with alternating GC base sequence: continuum treatment of salt effects.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

MONTY: a Monte Carlo approach to protein-DNA recognition.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1312361

Sequence and structural selectivity of nucleic acid binding ligands

28 November 2018

1 reference

12 December 2020

The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking

1 reference

12 December 2020

Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians

1 reference

12 December 2020

A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders

1 reference

12 December 2020

The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA

1 reference

12 December 2020

Energetics of drug-DNA interactions

1 reference

12 December 2020

An efficient molecular docking using conformational space annealing

1 reference

12 December 2020

Introducing a 4th dimension to protein-protein docking

1 reference

12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKI1008

1 reference

release_ymszj45nvfei3cpbqxlyzrfkku

5 July 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ymszj45nvfei3cpbqxlyzrfkku

24 November 2022

mapped directly with Wikidata item

PMC publication ID

1312361

1 reference

5 July 2017

1 reference