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Links tagged with 'gram-negative bacteria'

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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

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

PROFtmbTool Content

http://cubic.bioc.columbia.edu/services/proftmb/

Model Organisms > Microbes
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.

NAR Web Server Issue 2006
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tagsbacterial genome bacterial proteins gram-negative bacteria markov chains membrane proteins protein sequence analysis proteome proteomics reproducibility of results secondary protein structure sequence alignment

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