A threading-based method for the prediction of DNA-binding proteins with application to the human genome. (Q30382494)

16 October 2017

A threading-based method for the prediction of DNA-binding proteins with application to the human genome. (English)

1 reference

16 October 2017

2

Jeffrey Skolnick

1 reference

16 October 2017

Mu Gao

1

1 reference

16 October 2017

13 November 2009

1 reference

PLOS Computational Biology

16 October 2017

1 reference

16 October 2017

5

1 reference

16 October 2017

11

1 reference

16 October 2017

e1000567

1 reference

Creative Commons Attribution 4.0 International

16 October 2017

start time

13 November 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions

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Human genomic Z-DNA segments probed by the Z alpha domain of ADAR1.

20 June 2018

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The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ ADAR1

20 June 2018

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DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

20 June 2018

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The complete genome of an individual by massively parallel DNA sequencing

20 June 2018

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Single-molecule DNA sequencing of a viral genome

20 June 2018

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Regulation of innate immune responses by DAI (DLM-1/ZBP1) and other DNA-sensing molecules

20 June 2018

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The protein-binding potential of C2H2 zinc finger domains

20 June 2018

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ConFunc--functional annotation in the twilight zone

20 June 2018

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Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains

20 June 2018

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A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

20 June 2018

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The Pfam protein families database

20 June 2018

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Predicting protein function from sequence and structure

20 June 2018

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Prediction of DNA-binding residues from sequence

20 June 2018

1 reference

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DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile

20 June 2018

1 reference

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Barrier-to-autointegration factor--a BAFfling little protein

20 June 2018

1 reference

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DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Role of the Orc6 protein in origin recognition complex-dependent DNA binding and replication in Drosophila melanogaster

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Sticky fingers: zinc-fingers as protein-recognition motifs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Predicting DNA-binding sites of proteins from amino acid sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

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

20 June 2018

1 reference

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The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

The Universal Protein Resource (UniProt): an expanding universe of protein information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Kernel-based machine learning protocol for predicting DNA-binding proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Accurate multiplex polony sequencing of an evolved bacterial genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Genome sequencing in microfabricated high-density picolitre reactors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Predicting protein function from sequence and structural data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Protein-DNA recognition patterns and predictions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

TM-align: a protein structure alignment algorithm based on the TM-score

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

PSSM-based prediction of DNA binding sites in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Finishing the euchromatic sequence of the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Moment-based prediction of DNA-binding proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Prediction of protein function from protein sequence and structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Assessment of genome-wide protein function classification for Drosophila melanogaster

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Sequence-independent DNA binding and replication initiation by the human origin recognition complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

A cytokinetic function of Drosophila ORC6 protein resides in a domain distinct from its replication activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Annotating nucleic acid-binding function based on protein structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Enzyme function less conserved than anticipated.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

The origin recognition complex: from simple origins to complex functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

An overview of the structures of protein-DNA complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Gene ontology: tool for the unification of biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

From genes to protein structure and function: novel applications of computational approaches in the genomic era.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

20 June 2018

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=2770119

Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

CATH--a hierarchic classification of protein domain structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Cloning and functional characterization of Roaz, a zinc finger protein that interacts with O/E-1 to regulate gene expression: implications for olfactory neuronal development

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Protein structure comparison by alignment of distance matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Hidden Markov models in computational biology. Applications to protein modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

SCOP: a structural classification of proteins database for the investigation of sequences and structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

Optimal alignments in linear space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

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

20 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2770119

20 June 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000567

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000567

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000567

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000567

Barrier-to-autointegration factor-like (BAF-L): a proposed regulator of BAF

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19911048

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000567

1 reference

16 October 2017

journals/ploscb/GaoS09a

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

16 October 2017

1 reference

PMCID

2770119