Hidden Markov models from molecular dynamics simulations on DNA. (Q34065469)

30 July 2017

Hidden Markov models from molecular dynamics simulations on DNA. (English)

1 reference

30 July 2017

Kelly M Thayer

1

1 reference

PubMed ID

12072566

30 July 2017

D L Beveridge

series ordinal

2

1 reference

PubMed ID

12072566

30 July 2017

language of work or name

English

0 references

publication date

18 June 2002

1 reference

Proceedings of the National Academy of Sciences of the United States of America

30 July 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

30 July 2017

99

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30 July 2017

13

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30 July 2017

8642-8647

1 reference

ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

DNA structure: what's in charge?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Optimization of nucleic acid sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

A DNA structural atlas for Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Nucleic acids: theory and computer simulation, Y2K.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

DNA bendability--a novel feature in E. coli promoter recognition.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Clues and consequences of DNA bending in transcription

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Characterization of prokaryotic and eukaryotic promoters using hidden Markov models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Hidden Markov models of biological primary sequence information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

A hidden Markov model that finds genes in E. coli DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Bending and curvature calculations in B-DNA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Crystal structure analysis of a complete turn of B-DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Helix stability in prokaryotic promoter regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

The DNA Helix and How it is Read

28 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

A tutorial on hidden Markov models and selected applications in speech recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Naturally occurring nucleosome positioning signals in human exons and introns

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

High-speed molecular mechanics searches for optimal DNA interaction sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Cyclic AMP receptor protein: role in transcription activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Multiple alignment using hidden Markov models

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124344

Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature

28 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.132148699

DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12072566

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.132148699

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference

PubMed ID

12072566