Transmembrane beta barrel detection software tools | Membrane protein data analysis
Transmembrane beta barrels are membrane proteins found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They are important for pore formation, membrane anchoring, and enzyme activity. These proteins are also often responsible for bacterial virulence. Transmembrane beta barrel prediction tools use amino acid sequences of protein and algorithms for prediction.
A web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. BASys uses more than 30 programs to determine nearly 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, reactions, and pathways. The textual annotations and images that are provided by BASys can be generated in approximately 16 hours for an average bacterial chromosome (5 Megabases. 5000 genes), or approximately 350 coding regions per hour.
Offers a platform for aligning two protein structures. ProTop first detects secondary structures and run two algorithms for generating β-sheet maps according to five possible methods and detecting various contacts as well as close β-barrels. Then, the program performs a dynamic programming coupled to a sheet maps orientations enumeration to align either the sheet topologies or the whole topologies of the submitted sequence.
A web server which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion.
Provides a membrane protein explorer. MPEx provides an extendable framework for physical and biological hydropathy analyses and for b-barrel identification screening. It provides three analysis modes of operation that include (i) physical scale hydropathy analysis, (ii) translocon-scale hydropathy analysis and (iii) b-barrel analysis. It also offers two utility modes that include (i) Totalizer for estimating the binding free energies of peptides to phosphatidylcholine interfaces and (ii) Data-Buffer Overlay, which allows storage and graphical comparisons of different sliding-window plots.
A program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral beta-barrel outer membrane protein. BOMP is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane beta-strands.
A web-server for discriminating outer membrane proteins and predicting their membrane spanning beta-strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins.
Predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. PROFtmb was tested on a representative set of known TMB and non-TMB proteins. It detects 50% of TMBs at 80% accuracy (z-score>=10) and 70% of TMBs at 35% accuracy (z-score >= 6). The tool uses a Hidden Markov Model (HMM) whose parameters are trained on a set of labelled sequence profiles, and which accepts sequence profiles as input for prediction.