High performance transcription factor-DNA docking with GPU computing (Q36051143)

11 August 2017

High performance transcription factor-DNA docking with GPU computing (English)

1 reference

11 August 2017

Jiadong Wu

1

1 reference

11 August 2017

Bo Hong

series ordinal

2

1 reference

11 August 2017

Takako Takeda

series ordinal

3

1 reference

11 August 2017

Jun-Tao Guo

series ordinal

4

1 reference

11 August 2017

21 June 2012

1 reference

11 August 2017

1 reference

11 August 2017

10 Suppl 1

1 reference

11 August 2017

S17

1 reference

Benchmarks for flexible and rigid transcription factor-DNA docking

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Targeting Sp1 transcription factors in prostate cancer therapy.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Targeting transcription factor Stat5a/b as a therapeutic strategy for prostate cancer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

GPU accelerated biochemical network simulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

GPU computing for systems biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Mechanisms of transcription factor selectivity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Prediction of TF target sites based on atomistic models of protein-DNA complexes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Ab initio prediction of transcription factor targets using structural knowledge

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

UniProt: the Universal Protein knowledgebase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Transcription factors as targets for cancer therapy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Gene ontology: tool for the unification of biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

2 October 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

GBOOST: a GPU-based tool for detecting gene–gene interactions in genome–wide case control studies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3380734

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

11 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1477-5956-10-S1-S17

Conformational and physicochemical DNA features specific for transcription factor binding sites

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1477-5956-10-S1-S17

Ultra-fast FFT protein docking on graphics processors

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1477-5956-10-S1-S17

10.1186/1477-5956-10-S1-S17

21 January 2018

Identifiers

DOI

1 reference

Dimensions Publication ID

11 August 2017

0 references

1 reference

11 August 2017

PubMed publication ID

22759575

1 reference