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TMBpro specifications

Information


Unique identifier OMICS_07276
Name TMBpro
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TMBpro

TMBpro citations

 (5)
library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] n recognition and then evaluate the prediction probabilities (e.g. for helices HMMTOP , ENSEMBLE , Philius , TMHMM , MEMSAT-SVM , TOPCONS , PredαTM and for barrels B2TMPRED , ConBBPRED , PRED-TMBB , TMBpro , PredβTM , TMBHMM etc.). Machine learning approaches are best for solving problems in the absence of general theories when there is a large amount of data with noisy patterns and are thus ide […]

library_books

FmvB: A Francisella tularensis Magnesium Responsive Outer Membrane Protein that Plays a Role in Virulence

2016
PLoS One
PMCID: 4981453
PMID: 27513341
DOI: 10.1371/journal.pone.0160977

[…] ort processes, as outer membrane transport proteins in other bacteria are known to contain large extracellular loops []. Three-dimensional structural predictions of FmvA and FmvB were generated using TMBpro (Fig A in ). For FmvA, 8 beta strands were predicted and for FmvB 9 beta strands were predicted. However, for both proteins, TMBpro predicted long N-terminal unstructured regions (Fig A in ) th […]

call_split

A 3 Dimensional Trimeric β Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram Negative Bacterial Porins

2013
PLoS One
PMCID: 3723809
PMID: 23935908
DOI: 10.1371/journal.pone.0068934
call_split See protocol

[…] ember 2, 2011. This consensus sequence is identical at the amino acid level to that of isolate CS-362-07 (GenBank accession DQ116399). This sequence, excluding the first 22 residues, was submitted to TMBpro server (http://www.igb.uci.edu/~baldig/tmb.html) . Additional submissions were made excluding residues (i) A226–A238 and L290 - D316, (ii) A64–A 83 and L290 – D316 or (iii) A64 – P85, K152 – A1 […]

call_split

Fine Analysis of Genetic Diversity of the tpr Gene Family among Treponemal Species, Subspecies and Strains

2013
PLoS Negl Trop Dis
PMCID: 3656149
PMID: 23696912
DOI: 10.1371/journal.pntd.0002222
call_split See protocol

[…] alignment program . GenBank accession numbers are listed in . Structural homologs were identified using the 3D jury approach . Structural (3D) models for TprC, TprD and TprI were generated using the TMBpro algorithm . The orientation of the predicted loops in the TMBpro models, surface exposed vs. periplasmic, was determined as previously described by Randall et al. . Signal peptide predictions w […]

call_split

A graph theoretic approach for classification and structure prediction of transmembrane β barrel proteins

2012
BMC Genomics
PMCID: 3394416
PMID: 22537300
DOI: 10.1186/1471-2164-13-S2-S5
call_split See protocol

[…] We compare our folding prediction accuracy to TMBpro [] and TMBETAPRED-RBF []. We compare our classification results to Freeman et al. [], TMBETAPRED-RBF [], PRED-TMBB [] and transFold []. TMBpro and TMBETAPRED-RBF results are executed from their […]

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TMBpro institution(s)
School of Information and Computer Sciences, University of California, Irvine, CA, USA

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