(Q33481214)

27 July 2017

title

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures (English)

1 reference

27 July 2017

1 reference

RyangGuk Kim

1 reference

27 July 2017

Jun-tao Guo

series ordinal

1 reference

27 July 2017

language of work or name

English

0 references

publication date

7 July 2009

1 reference

27 July 2017

1 reference

27 July 2017

volume

10 Suppl 1

1 reference

27 July 2017

page(s)

S13

1 reference

Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species

27 July 2017

cites work

1 reference

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Gene regulation in the postgenomic era: technology takes the wheel

21 June 2018

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Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Prediction of DNA-binding residues from sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Efficient prediction of nucleic acid binding function from low-resolution protein structures.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

SCOP database in 2004: refinements integrate structure and sequence family data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

AANT: the Amino Acid-Nucleotide Interaction Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

A computational pipeline for protein structure prediction and analysis at genome scale.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

An overview of the structures of protein-DNA complexes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

21 June 2018

The Protein Data Bank

1 reference

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Structure-based prediction of DNA target sites by regulatory proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

DNA bending: the prevalence of kinkiness and the virtues of normality

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

RASMOL: biomolecular graphics for all

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Optimal alignments in linear space

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

A rigorous basepair oriented description of DNA structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Rapid and sensitive sequence comparison with FASTP and FASTA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Structures of ParB bound to DNA reveal mechanism of partition complex formation.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

The Assessment of the Geometry of Dinucleotide Steps in Double-Helical DNA; a New Local Calculation Scheme

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

Classification of Protein-DNA Complexes Based on Structural Descriptors

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2709256

B-DNA twisting correlates with base-pair morphology.

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19594872

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19594872

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A DNA-Centric Look at Protein-DNA Complexes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19594872

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-10-S1-S13

1 reference

Dimensions Publication ID

27 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-10-s1-s13

9 September 2019

1 reference

27 July 2017

1 reference