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Links tagged with 'membrane proteins'

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Found 32 links

Displaying 15 links

Berkeley Drosophila Genome ProjectResource Content

http://www.fruitfly.org/

Model Organisms > Fly

Good entrez to fly genome resources.

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tagsamino acid sequence animals base sequence cell line cluster analysis complementary dna dna sequence analysis drosophila melanogaster expressed sequence tags gene library genetic databases genome insect genes male membrane glycoproteins membrane proteins molecular sequence data rna sequence alignment testis

BRENDA - The Comprehensive Enzyme Information SystemDatabase Content

http://www.brenda-enzymes.org/

Protein > Interactions, Pathways, Enzymes

Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.

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tagsanimals enzymes factual databases genomics humans ligands membrane proteins organ specificity protein conformation protein databases protein transport rats substrate specificity systems integration terminology as topic

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

MeMotifDatabase Content

http://projects.biotec.tu-dresden.de/memotif

Protein > Databases

MeMotif is a database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable.

NAR Database Issue 2010
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tagsamino acid motifs bacterial proteins computational biology genetic databases membrane proteins nucleic acid databases protein databases secondary protein structure tertiary protein structure

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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tagsamino acid sequence homology gpi-linked proteins membrane proteins molecular sequence annotation protein sorting signals tertiary protein structure

MolAxisTool Content

http://bioinfo3d.cs.tau.ac.il/MolAxis

Protein > 3-D Structural Features

The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological transport computational biology membrane proteins molecular models nucleic acids

MPlotTool Content

http://proteinformatics.charite.de/mplot/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.

NAR Web Server Issue 2010
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tagsmembrane proteins molecular models secondary protein structure tertiary protein structure

PatchDockTool Content

http://bioinfo3d.cs.tau.ac.il/PatchDock/

Protein > Molecular Dynamics and Docking

PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

NAR Web Server Issue 2005
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tagsalgorithms alpha-amylases antibodies antigen receptors bacterial proteins binding sites capsid proteins computational biology exotoxins influenza virus hemagglutinin glycoproteins ligands macromolecular substances membrane proteins molecular models multiprotein complexes phosphoenolpyruvate sugar phosphotransferase system protein conformation protein interaction mapping protein-serine-threonine kinases proteins secondary protein structure viral antigens

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

NAR Web Server Issue 2006
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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

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

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

PONGOTool Content

http://pongo.biocomp.unibo.it/

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

PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.

NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence automated pattern recognition humans lipoproteins membrane proteins neural networks (computer) protein conformation protein sequence analysis protein sorting signals reproducibility of results sensitivity and specificity sequence alignment

PRALINETool Content

http://ibivu.cs.vu.nl/programs/pralinewww/

Protein > 2-D Structure Prediction
Sequence Comparison > Multiple Sequence Alignments

Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.

NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms amino acid motifs amino acid sequence amino acid sequence homology amino acids bacterial proteins binding sites cluster analysis computational biology consensus sequence cytochrome p-450 enzyme system database management systems discriminant analysis flavodoxin genetic databases hiv integrase membrane proteins molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment systems integration tertiary protein structure

PRED-TMBBTool Content

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

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

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.

This content is being maintained by pbagos.

NAR Web Server Issue 2004
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tagsbacterial outer membrane proteins escherichia coli proteins gram-negative bacteria hidden markov model markov chains membrane proteins peptides predictive value of tests protein databases protein sequence analysis secondary protein structure statistical models tertiary protein structure topology prediction