> > Localization and Targeting

Localization and Targeting

This section contains links to tools related to predicting subcellular localization, the presence of transmembrane regions, and/or targeting including the prediction of signal peptides.

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Found 37 links

Displaying 15 links

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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BOMPTool Content

http://www.bioinfo.no/tools/bomp

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

NAR Web Server Issue 2004
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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

ESLpredTool Content

http://www.imtech.res.in/raghava/eslpred/

Protein > Localization and Targeting

ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.

This content is being maintained by raghavagps.

NAR Web Server Issue 2004
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tagsartificial intelligence dipeptides eukaryotic cells protein databases proteins reproducibility of results

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

NAR Web Server Issue 2007
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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

GPCRsclassTool Content

http://www.imtech.res.in/raghava/gpcrsclass/

Protein > Annotation and Function
Protein > Localization and Targeting

GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.

This content is being maintained by raghavagps.

NAR Web Server Issue 2005
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tagsadrenergic receptors artificial intelligence biogenic amine receptors cholinergic receptors dipeptides dopamine receptors g-protein-coupled receptors protein sequence analysis serotonin receptors

Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/

Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

NAR Web Server Issue 2006
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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

LOCATEDatabase Content

http://locate.imb.uq.edu.au/

Model Organisms > Mouse and Rat
Protein > Localization and Targeting

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.

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tagsanimals membrane proteins mice protein databases protein isoforms proteome

MemPypeTool Content

http://mu2py.biocomp.unibo.it/mempype

Computer Related > Workflows
Protein > Localization and Targeting

MemPype is a Python-based pipeline that integrates several tools for the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

NAR Web Server Issue 2011
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MetaMHCTool Content

http://www.biokdd.fudan.edu.cn/Service/MetaMHC.html

Human Genome > Annotations
Protein > Domains and Motifs
Protein > Localization and Targeting

MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.

This content is being maintained by Xihao Hu.

NAR Web Server Issue 2010
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tagsanimals binding sites histocompatibility antigens class i histocompatibility antigens class ii humans mice peptides

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start...

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

NAR Web Server Issue 2007
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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

PA-SUBTool Content

http://www.cs.ualberta.ca/~bioinfo/PA/Sub/

Protein > Localization and Targeting

PA-SUB (Proteome Analyst Specialized Subcellular Localization Server) can be used to predict the subcellular localization of proteins using established machine learning techniques.

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tagsalgorithms amino acid sequence homology artificial intelligence automated pattern recognition cellular structures cluster analysis natural language processing protein databases protein sequence analysis proteins proteome proteomics reproducibility of results sequence alignment tissue distribution

PhobiusTool Content

http://phobius.sbc.su.se/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

Tags associated with subcategory 'Protein/Localization and Targeting'

protein sequence analysis reproducibility of results membrane proteins secondary protein structure algorithms protein databases proteins animals humans computational biology sequence alignment amino acid sequence molecular models neural networks (computer) molecular sequence data eukaryotic cells protein sorting signals proteome bacterial outer membrane proteins statistical models proteomics tertiary protein structure artificial intelligence protein conformation chemical models polypyrimidine tract-binding protein software design probability peptide fragments open reading frames genome genomics london mathematics biological models rhodopseudomonas computer simulation molecular evolution computer security database management systems double-blind method porins markov chains haemophilus influenzae forecasting peptides sensitivity and specificity evaluation studies as topic escherichia coli decision trees cell membrane cytoplasm expert systems factual databases saccharomyces cerevisiae protein precursors lipoproteins fungal proteins gram-negative bacteria binding sites bayes theorem subcellular fractions salmonella typhimurium theoretical models sequence homology structural models drosophila nucleic acid sequence homology tissue plasminogen activator thermodynamics sequence analysis proto-oncogene proteins c-myc protein folding genetic databases gene expression profiling genetic models programming languages gene expression regulation fungal genes membrane transport proteins amino acid sequence homology rats automated pattern recognition prokaryotic cells dna methylation dna primers cysteine conserved sequence mice capsid proteins cell line bacterial proteins protein transport acyltransferases amino acid motifs cell compartmentation arabidopsis escherichia coli proteins hidden markov model predictive value of tests adrenergic receptors