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Links tagged with 'rna-binding proteins'

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AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite

RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

NAR Database Issue 2011
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tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

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

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

CLIPZDatabase Content

http://www.clipz.unibas.ch

RNA > Databases

CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.

This content is being maintained by nonb@nih.gov.

NAR Database Issue 2011
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tagsanimals binding sites genetic databases genome humans messenger rna mice rna sequence analysis rna-binding proteins transfer rna untranslated rna

ESEfinderTool Content

http://rulai.cshl.edu/tools/ESE/

Expression > Splicing

ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.

NAR Web Server Issue 2003
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tagsbase sequence consensus sequence exons genetic enhancer elements humans messenger rna point mutation rna precursors rna sequence analysis rna splicing rna-binding 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

NAPSTool Content

http://proteomics.bioengr.uic.edu/NAPS

Protein > Sequence Features

NAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.

NAR Web Server Issue 2010
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tagsalgorithms binding sites dna-binding proteins protein sequence analysis reproducibility of results rna-binding proteins

PI2PETool Content

http://pipe.scs.fsu.edu/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

PiRaNhATool Content

http://www.bioinformatics.sussex.ac.uk/PIRANHA

Protein > Sequence Features

The PiRaNhA web server predicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.

NAR Web Server Issue 2010
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tagsalgorithms artificial intelligence binding sites computational biology protein databases protein sequence analysis rna rna-binding proteins

PRIDBDatabase Content

http://bindr.gdcb.iastate.edu/PRIDB

Protein > Databases
RNA > Databases

The Protein-RNA Interface Database (PRIDB) is a database of protein-RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein-RNA complexes and their interfaces, in addition to automated generation of user-defined data sets of protein-RNA interfaces for statistical analyses and machine learning applications. For any chosen PDB complex or list of complexes, PRIDB rapidly displays interfacial amino acids and ribonucleotides within the primary sequences of the interacting protein and RNA chains. PRIDB also identifies ProSite motifs in protein chains and FR3D motifs in RNA chains and provides links to these external databases, as well as to structure files in the PDB. An integrated JMol applet is provided for visualization of interacting atoms and residues in the context of the 3D complex structures. Atomic- and residue-level contact information for the entire data set can be downloaded in a simple machine-readable format.

This content is being maintained by balewis.

NAR Database Issue 2011
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tagsamino acids binding sites nucleic acid conformation protein conformation protein databases ribonucleotides rna rna-binding proteins

RBPDBDatabase Content

http://rbpdb.ccbr.utoronto.ca/

RNA > Databases

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites.

NAR Database Issue 2011
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tagsanimals binding sites caenorhabditis elegans proteins drosophila proteins humans messenger rna mice protein databases rna sequence analysis rna-binding proteins tertiary protein structure
setsUniversity of Toronto

SFmapTool Content

http://sfmap.technion.ac.il

DNA > Structure and Sequence Feature Detection

SFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.

NAR Web Server Issue 2010
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tagsalgorithms alternative splicing binding sites human genome humans rna sequence analysis rna-binding proteins

starBaseDatabase Content

http://starbase.sysu.edu.cn/

RNA > Databases

StarBase (sRNA target Base) facilitates the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. Two web servers are provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways.

NAR Database Issue 2011
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tagsanimals binding sites gene expression regulation genomics humans messenger rna mice micrornas nucleic acid databases rna sequence analysis rna-binding proteins