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Links tagged with 'bacterial outer membrane proteins'

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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

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

NAR Web Server Issue 2003NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

HHompTool Content

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

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.

This content is being maintained by mremmert.

NAR Web Server Issue 2009
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tagsamino acid sequence homology bacterial outer membrane proteins escherichia coli proteins protein databases

OMPdbDatabase Content

http://bioinformatics.biol.uoa.gr/OMPdb

Protein > Databases

OMPdb is a database of integral beta-barrel outer membrane proteins from Gram-negative bacteria, classified in functional families. OMPdb entries contain cross-references to other databases, references to the literature and annotation for sequence features (TM segments and signal peptides). The user can submit text searches and run BLAST queries against protein sequences or domain searches against the collection of profile HMMs that represent each family's domain organization.

This content is being maintained by pbagos.

NAR Database Issue 2011
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tagsbacterial outer membrane proteins gram-negative bacteria protein databases 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

PSORT.orgTool Content

http://www.psort.org/

Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

TMBETA-NETTool Content

http://psfs.cbrc.jp/tmbeta-net/

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

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acids bacterial outer membrane proteins cell membrane factual databases membrane proteins molecular models neural networks (computer) reproducibility of results secondary protein structure

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/

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

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

transFoldTool Content

http://bioinformatics.bc.edu/clotelab/transFold

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

transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.

NAR Web Server Issue 2006
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tagsamino acids bacterial outer membrane proteins membrane proteins secondary protein structure