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Links tagged with 'dna-binding proteins'

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Found 36 links

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3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint

DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology dna-binding proteins genetic databases genetic regulation humans nucleic acid databases protein conformation protein databases protein-DNA complex pubmed regulator genes sequence alignment

BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

NAR Web Server Issue 2006
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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

BIOBASE Gene Regulation databasesDatabase Content

http://www.gene-regulation.com/pub/databases.html

Protein > Interactions, Pathways, Enzymes

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

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tagsanimals binding sites chromatin chromosomes database management systems developmental gene expression regulation dna-binding proteins eukaryotic cells forecasting gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans macromolecular substances mice nuclear matrix nuclear proteins nucleic acid databases oligonucleotide array sequence analysis protein databases saccharomyces signal transduction systems integration tissue distribution transcription factors

Blocks WWW ServerTool Content

http://blocks.fhcrc.org/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

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tagsadenosine triphosphatases algorithms amino acid sequence amino acid sequence homology animals computational biology dna helicases dna-binding proteins factual databases humans molecular sequence data nuclear proteins proteins sequence alignment software design transcription factors

CCRXPTool Content

http://ccrxp.netasa.org

Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

This content is being maintained by shandar.

NAR Web Server Issue 2010
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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

CONREALTool Content

http://conreal.niob.knaw.nl/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

DNABINDPROTTool Content

http://www.prc.boun.edu.tr/appserv/prc/dnabindprot

DNA > Structure and Sequence Feature Detection

DNABINDPROT web tool is designed to predict DNA-binding residues in high frequency modes by the Gaussian network method.

NAR Web Server Issue 2010
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tagsbinding sites cyclic amp receptor protein dna-binding proteins

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

enoLOGOSTool Content

http://biodev.hgen.pitt.edu/enologos/

Sequence Comparison > Alignment Editing and Visualization

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

NAR Web Server Issue 2005
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tagsamino acids binding sites dna sequence analysis dna-binding proteins sequence alignment zinc fingers

ESPriptTool Content

http://espript.ibcp.fr/ESPript/ESPript/index.php

Sequence Comparison > Alignment Editing and Visualization

Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology dna-binding proteins molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

Interolog/Regulog DatabaseDatabase Content

http://interolog.gersteinlab.org/

Model Organisms > Fly
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

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tagsamino acid sequence amino acid sequence homology animals bacterial dna bacterial genome bacterial proteins binding sites caenorhabditis elegans caenorhabditis elegans proteins computational biology conserved sequence dna dna-binding proteins drosophila melanogaster drosophila proteins fungal dna fungal genome genome helicobacter pylori helminth dna protein binding protein databases protein interaction mapping proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins binding sites carrier proteins conserved sequence dna-binding proteins factual databases genetic variation glucocorticoid receptors haemophilus influenzae humans molecular evolution molecular models molecular sequence data mutation phylogeny protein conformation proteins quaternary protein structure rats rna-binding proteins sequence alignment src homology domains streptococcus pneumoniae zinc fingers

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

NAR Web Server Issue 2004
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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors