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1.  PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins 
Nucleic Acids Research  2006;34(Web Server issue):W186-W188.
PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward- and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at .
doi:10.1093/nar/gkl262
PMCID: PMC1538807  PMID: 16844988
2.  transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels 
Nucleic Acids Research  2006;34(Web Server issue):W189-W193.
Transmembrane β-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts. The cellular location and functional diversity of β-barrel outer membrane proteins makes them an important protein class. At the present time, very few non-homologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane (TM) proteins. The transFold web server uses pairwise inter-strand residue statistical potentials derived from globular (non-outer-membrane) proteins to predict the supersecondary structure of TMB. Unlike all previous approaches, transFold does not use machine learning methods such as hidden Markov models or neural networks; instead, transFold employs multi-tape S-attribute grammars to describe all potential conformations, and then applies dynamic programming to determine the global minimum energy supersecondary structure. The transFold web server not only predicts secondary structure and TMB topology, but is the only method which additionally predicts the side-chain orientation of transmembrane β-strand residues, inter-strand residue contacts and TM β-strand inclination with respect to the membrane. The program transFold currently outperforms all other methods for accuracy of β-barrel structure prediction. Available at .
doi:10.1093/nar/gkl205
PMCID: PMC1538872  PMID: 16844989
3.  A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins 
BMC Genomics  2012;13(Suppl 2):S5.
Background
Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have been introduced for recognition and structure prediction of transmembrane β-barrel proteins. Most of these methods emphasize on homology search rather than any biological or chemical basis.
Results
We present a novel graph-theoretic model for classification and structure prediction of transmembrane β-barrel proteins. This model folds proteins based on energy minimization rather than a homology search, avoiding any assumption on availability of training dataset. The ab initio model presented in this paper is the first method to allow for permutations in the structure of transmembrane proteins and provides more structural information than any known algorithm. The model is also able to recognize β-barrels by assessing the pseudo free energy. We assess the structure prediction on 41 proteins gathered from existing databases on experimentally validated transmembrane β-barrel proteins. We show that our approach is quite accurate with over 90% F-score on strands and over 74% F-score on residues. The results are comparable to other algorithms suggesting that our pseudo-energy model is close to the actual physical model. We test our classification approach and show that it is able to reject α-helical bundles with 100% accuracy and β-barrel lipocalins with 97% accuracy.
Conclusions
We show that it is possible to design models for classification and structure prediction for transmembrane β-barrel proteins which do not depend essentially on training sets but on combinatorial properties of the structures to be proved. These models are fairly accurate, robust and can be run very efficiently on PC-like computers. Such models are useful for the genome screening.
doi:10.1186/1471-2164-13-S2-S5
PMCID: PMC3394416  PMID: 22537300
4.  A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins 
BMC Bioinformatics  2004;5:29.
Background
Integral membrane proteins constitute about 20–30% of all proteins in the fully sequenced genomes. They come in two structural classes, the α-helical and the β-barrel membrane proteins, demonstrating different physicochemical characteristics, structure and localization. While transmembrane segment prediction for the α-helical integral membrane proteins appears to be an easy task nowadays, the same is much more difficult for the β-barrel membrane proteins. We developed a method, based on a Hidden Markov Model, capable of predicting the transmembrane β-strands of the outer membrane proteins of gram-negative bacteria, and discriminating those from water-soluble proteins in large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of correct predictions rather than the likelihood of the sequences.
Results
The training has been performed on a non-redundant database of 14 outer membrane proteins with structures known at atomic resolution; it has been tested with a jacknife procedure, yielding a per residue accuracy of 84.2% and a correlation coefficient of 0.72, whereas for the self-consistency test the per residue accuracy was 88.1% and the correlation coefficient 0.824. The total number of correctly predicted topologies is 10 out of 14 in the self-consistency test, and 9 out of 14 in the jacknife. Furthermore, the model is capable of discriminating outer membrane from water-soluble proteins in large-scale applications, with a success rate of 88.8% and 89.2% for the correct classification of outer membrane and water-soluble proteins respectively, the highest rates obtained in the literature. That test has been performed independently on a set of known outer membrane proteins with low sequence identity with each other and also with the proteins of the training set.
Conclusion
Based on the above, we developed a strategy, that enabled us to screen the entire proteome of E. coli for outer membrane proteins. The results were satisfactory, thus the method presented here appears to be suitable for screening entire proteomes for the discovery of novel outer membrane proteins. A web interface available for non-commercial users is located at: , and it is the only freely available HMM-based predictor for β-barrel outer membrane protein topology.
doi:10.1186/1471-2105-5-29
PMCID: PMC385222  PMID: 15070403
5.  TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins 
BMC Bioinformatics  2005;6:56.
Background
Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes.
Results
We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure.
A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings.
Conclusion
TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection.
doi:10.1186/1471-2105-6-56
PMCID: PMC1274253  PMID: 15769290
6.  PRED-TMBB: a web server for predicting the topology of β-barrel outer membrane proteins 
Nucleic Acids Research  2004;32(Web Server issue):W400-W404.
The β-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for α-helical membrane proteins, currently there is no freely available prediction method for β-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of β-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. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane β-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer.
doi:10.1093/nar/gkh417
PMCID: PMC441555  PMID: 15215419
7.  Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method 
BMC Bioinformatics  2005;6:7.
Background
Prediction of the transmembrane strands and topology of β-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of β-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 β-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method.
Results
We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane β-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies.
Conclusions
The consensus prediction method described in this work, optimizes the predicted topology with a dynamic programming algorithm and is implemented in a web-based application freely available to non-commercial users at .
doi:10.1186/1471-2105-6-7
PMCID: PMC545999  PMID: 15647112
8.  SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone 
Bioinformatics  2012;28(9):1216-1222.
Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related has been profile hidden Markov models (HMMs). However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta sheets. These dependencies have been partially captured in the HMM setting by simulated evolution in the training phase and can be fully captured by Markov random fields (MRFs). However, the MRFs can be computationally prohibitive when beta strands are interleaved in complex topologies. We introduce SMURFLite, a method that combines both simplified MRFs and simulated evolution to substantially improve remote homology detection for beta structures. Unlike previous MRF-based methods, SMURFLite is computationally feasible on any beta-structural motif.
Results: We test SMURFLite on all propeller and barrel folds in the mainly-beta class of the SCOP hierarchy in stringent cross-validation experiments. We show a mean 26% (median 16%) improvement in area under curve (AUC) for beta-structural motif recognition as compared with HMMER (a well-known HMM method) and a mean 33% (median 19%) improvement as compared with RAPTOR (a well-known threading method) and even a mean 18% (median 10%) improvement in AUC over HHPred (a profile–profile HMM method), despite HHpred's use of extensive additional training data. We demonstrate SMURFLite's ability to scale to whole genomes by running a SMURFLite library of 207 beta-structural SCOP superfamilies against the entire genome of Thermotoga maritima, and make over a 100 new fold predictions.
Availability and implementaion: A webserver that runs SMURFLite is available at: http://smurf.cs.tufts.edu/smurflite/
Contact: lenore.cowen@tufts.edu; bab@mit.edu
doi:10.1093/bioinformatics/bts110
PMCID: PMC3338012  PMID: 22408192
9.  Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions 
Bioinformatics  2012;28(12):i90-i96.
Motivation: Transmembrane β-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few β-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful.
Results: Here, we present tobmodel; a method for generating 3D models of β-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the β-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average error of 1.61 Å. Tobmodel predicts the correct topology for 75% of the proteins in the dataset which is a slight improvement over BOCTOPUS alone. More importantly, however, tobmodel provides a Cα template with an average RMSD of 7.24 Å from the native structure.
Availability: Tobmodel is freely available as a web server at: http://tobmodel.cbr.su.se/. The datasets used for training and evaluations are also available from this site.
Contact: arne@bioinfo.se
doi:10.1093/bioinformatics/bts233
PMCID: PMC3371865  PMID: 22689784
10.  TMB-Hunt: a web server to screen sequence sets for transmembrane β-barrel proteins 
Nucleic Acids Research  2005;33(Web Server issue):W188-W192.
TMB-Hunt is a program that uses a modified k-nearest neighbour (k-NN) algorithm to classify protein sequences as transmembrane β-barrel (TMB) or non-TMB on the basis of whole sequence amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, a discrimination accuracy of 92.5% was achieved, as tested using a rigorous cross-validation procedure. The TMB-Hunt web server, available at , allows screening of up to 10 000 sequences in a single query and provides results and key statistics in a simple colour coded format.
doi:10.1093/nar/gki384
PMCID: PMC1160145  PMID: 15980452
11.  Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins 
Beta-barrel membrane proteins (MP) are found in Gram-negative bacteria, mitochondria and chloroplasts. They play important roles in metabolism of bacteria, where they are involved in transport of solutes in and out of the cell. Beta-barrel proteins may also act as proteases, lipases and may be important for cell-cell adhesion. Currently, there are about 30 non-redundant solved structures of β-barrels. Although the number of b-barrel folds is fairly small, it is possible to expand the amount of available structural information by homology modeling using existing structures as templates. The scope of structure prediction may be widened by finding remote homologues of the existing structures. To improve the sensitivity of the database searches and the quality of sequence alignments, we first study evolutionary history of transmembrane segments of 7 β-barrel membrane proteins by estimating substitution rates with a Bayesian Monte Carlo approach. Next, we calculate amino acid substitution matrices, beta-barrel Transmembrane scoring Matrices (bbTM), specifically tuned for TM regions, which can be used to detect remote homologues. We then test bbTM matrices by comparing their performance with membrane-protein derived scoring matrices PHAT and SLIM. Our results demonstrate that bbTM matrices have higher selectivity towards transmembrane β-barrel proteins and may be used with higher confidence in database searches for remote homologues of this class of proteins.
PMCID: PMC2630510  PMID: 19162917
Substitution rate; scoring matrices; beta barrel membrane proteins; bioinformatics
12.  Hidden markov model for the prediction of transmembrane proteins using MATLAB 
Bioinformation  2011;7(8):418-421.
Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy.
Availability
The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in
PMCID: PMC3280443  PMID: 22347785
Hidden Markov Model; Transmembrane Proteins; MATLAB
13.  Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins 
β-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They are important for pore formation, membrane anchoring, enzyme activity, and are often responsible for bacterial virulence. Due to difficulties in experimental structure determination, they are sparsely represented in the protein structure databank. We have developed a computational method for predicting structures of the trans-membrane (TM) domains of β-barrel membrane proteins. Our method based on key organization principles, can predict structures of the TM domain of β-barrel membrane proteins of novel topology, including those from eukaryotic mitochondria. Our method is based on a model of physical interactions, a discrete conformational state-space, an empirical potential function, as well as a model to account for interstrand loop entropy. We are able to construct three dimensional atomic structure of the TM-domains from sequences for a set of 23 non-homologous proteins (resolution 1.8 – 3.0 Å). The median RMSD of TM-domains containing 75–222 residues between predicted and measured structures is 3.9 Å for main chain atoms. In addition, stability determinants and protein-protein interaction sites can be predicted. Such predictions on eukaryotic mitochondria outer membrane protein Tom40 and VDAC are confirmed by independent mutagenesis and chemical cross-linking studies. These results suggest that our model captures key components of the organization principles of β-barrel membrane protein assembly.
doi:10.1021/ja209895m
PMCID: PMC3415959  PMID: 22148174
14.  BOMP: a program to predict integral β-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria 
Nucleic Acids Research  2004;32(Web Server issue):W394-W399.
This work describes the development of a program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral β-barrel outer membrane protein. The program, called the β-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral β-barrel proteins. The first component is a C-terminal pattern typical of many integral β-barrel proteins. The second component calculates an integral β-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane β-strands. The precision of the predictions was found to be 80% with a recall of 88% when tested on the proteins with SwissProt annotated subcellular localization in Escherichia coli K 12 (788 sequences) and Salmonella typhimurium (366 sequences). When tested on the predicted proteome of E.coli, BOMP found 103 of a total of 4346 polypeptide sequences to be possible integral β-barrel proteins. Of these, 36 were found by BLAST to lack similarity (E-value score < 1e−10) to proteins with annotated subcellular localization in SwissProt. BOMP predicted the content of integral β-barrels per predicted proteome of 10 different bacteria to range from 1.8 to 3%. BOMP is available at http://www.bioinfo.no/tools/bomp.
doi:10.1093/nar/gkh351
PMCID: PMC441489  PMID: 15215418
15.  The prediction and characterization of YshA, an unknown outer membrane protein from Salmonella typhimurium 
Biochimica et biophysica acta  2010;1808(1):287-297.
We have developed an effective pathway for the prediction and characterization of novel transmembrane β-barrel proteins. The Freeman-Wimley algorithm, which is a highly accurate prediction method based on the physicochemical properties of experimentally characterized transmembrane β barrel (TMBB) structures, was used to predict TMBBs in the genome of Salmonella typhimurium LT2. The previously uncharacterized product of gene yshA was tested as a model for validating the algorithm. YshA is a highly conserved 230-residue protein that is predicted to have 10 transmembrane β-strands and an N-terminal signal sequence. All of the physicochemical and spectroscopic properties exhibited by YshA are consistent with the prediction that it is a TMBB. Specifically, recombinant YshA localizes to the outer membrane when expressed in Escherichia coli; YshA has β-sheet-rich secondary structure with stable tertiary contacts in the presence of detergent micelles or when reconstituted into a lipid bilayer; when in a lipid bilayer, YshA forms a membrane-spanning pore with an effective radius of ~0.7 nm. Taken together, these data substantiate the predictions made by the Freeman-Wimley algorithm by showing that YshA is a TMBB protein.
doi:10.1016/j.bbamem.2010.09.008
PMCID: PMC2997857  PMID: 20863811
16.  Membrane protein orientation and refinement using a knowledge-based statistical potential 
BMC Bioinformatics  2013;14:276.
Background
Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment, which is otherwise challenging to investigate using experimental techniques due to the difficulty in crystallising membrane proteins embedded within intact membranes.
Results
We have developed a knowledge-based membrane potential, calculated by the statistical analysis of transmembrane protein structures, coupled with a combination of genetic and direct search algorithms, and demonstrate its use in positioning proteins in membranes, refinement of membrane protein models and in decoy discrimination.
Conclusions
Our method is able to quickly and accurately orientate both alpha-helical and beta-barrel membrane proteins within the lipid bilayer, showing closer agreement with experimentally determined values than existing approaches. We also demonstrate both consistent and significant refinement of membrane protein models and the effective discrimination between native and decoy structures. Source code is available under an open source license from http://bioinf.cs.ucl.ac.uk/downloads/memembed/.
doi:10.1186/1471-2105-14-276
PMCID: PMC3852961  PMID: 24047460
Membrane protein; Statistical potential; Orientation; Refinement; Genetic algorithm
17.  TMBB-DB: a transmembrane β-barrel proteome database 
Bioinformatics  2012;28(19):2425-2430.
Motivation: We previously reported the development of a highly accurate statistical algorithm for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from genomic sequence data of Gram-negative bacteria (Freeman,T.C. and Wimley,W.C. (2010) Bioinformatics, 26, 1965–1974). We have now applied this identification algorithm to all available Gram-negative bacterial genomes (over 600 chromosomes) and have constructed a publicly available, searchable, up-to-date, database of all proteins in these genomes.
Results: For each protein in the database, there is information on (i) β-barrel membrane protein probability for identification of β-barrels, (ii) β-strand and β-hairpin propensity for structure and topology prediction, (iii) signal sequence score because most TMBBs are secreted through the inner membrane translocon and, thus, have a signal sequence, and (iv) transmembrane α-helix predictions, for reducing false positive predictions. This information is sufficient for the accurate identification of most β-barrel membrane proteins in these genomes. In the database there are nearly 50 000 predicted TMBBs (out of 1.9 million total putative proteins). Of those, more than 15 000 are ‘hypothetical’ or ‘putative’ proteins, not previously identified as TMBBs. This wealth of genomic information is not available anywhere else.
Availability: The TMBB genomic database is available at http://beta-barrel.tulane.edu/.
Contact: wwimley@tulane.edu
doi:10.1093/bioinformatics/bts478
PMCID: PMC3463127  PMID: 22843985
18.  Beta barrel trans-membrane proteins: Enhanced prediction using a Bayesian approach 
Bioinformation  2006;1(6):231-233.
Membrane proteins, which constitute approximately 20% of most genomes, form two main classes: alpha helical and beta barrel transmembrane proteins. Using methods based on Bayesian Networks, a powerful approach for statistical inference, we have sought to address β-barrel topology prediction. The β-barrel topology predictor reports individual strand accuracies of 88.6%. The method outlined here represents a potentially important advance in the computational determination of membrane protein topology.
PMCID: PMC1891693  PMID: 17597895
beta barrel transmembrane protein; prokaryotic membrane proteins; Bayesian Networks; prediction method; sub-cellular location
19.  TIM-Finder: A new method for identifying TIM-barrel proteins 
Background
The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.
Results
To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.
Conclusions
TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.
doi:10.1186/1472-6807-9-73
PMCID: PMC2803183  PMID: 20003393
20.  HHomp—prediction and classification of outer membrane proteins 
Nucleic Acids Research  2009;37(Web Server issue):W446-W451.
Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. Most prediction methods have focused on analogous features, such as alternating hydrophobicity patterns. Here, we start from the observation that almost all β-barrel OMPs are related by common ancestry. We identify proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20 000 putative OMP sequences. These were collected with the exhaustive, transitive homology detection method HHsenser, starting from 23 representative OMPs in the PDB database. In a benchmark on TransportDB, HHomp detects 63.5% of the true positives before including the first false positive. This is 70% more than PROFtmb, four times more than BOMP and 10 times more than TMB-Hunt. In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit.tuebingen.mpg.de/hhomp.
doi:10.1093/nar/gkp325
PMCID: PMC2703889  PMID: 19429691
21.  PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation 
Nucleic Acids Research  2008;36(Web Server issue):W202-W209.
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 Å RMSD). The average PROTEUS2 prediction takes ∼3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2.
doi:10.1093/nar/gkn255
PMCID: PMC2447806  PMID: 18483082
22.  The Prediction of Membrane Protein Structure and Genome Structural Annotation 
New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β-barrel and all-α membrane proteins with high accuracy and a low rate of false positives and false negatives. These methods have been integrated in a suite of programs to filter proteomes of Gram-negative bacteria, searching for new membrane proteins.
doi:10.1002/cfg.308
PMCID: PMC2447372  PMID: 18629086
23.  OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria 
Nucleic Acids Research  2010;39(Database issue):D324-D331.
We describe here OMPdb, which is currently the most complete and comprehensive collection of integral β-barrel outer membrane proteins from Gram-negative bacteria. The database currently contains 69 354 proteins, which are classified into 85 families, based mainly on structural and functional criteria. Although OMPdb follows the annotation scheme of Pfam, many of the families included in the database were not previously described or annotated in other publicly available databases. There are also cross-references to other databases, references to the literature and annotation for sequence features, like transmembrane segments and signal peptides. Furthermore, via the web interface, the user can not only browse the available data, but submit advanced text searches and run BLAST queries against the database protein sequences or domain searches against the collection of profile Hidden Markov Models that represent each family’s domain organization as well. The database is freely accessible for academic users at http://bioinformatics.biol.uoa.gr/OMPdb and we expect it to be useful for genome-wide analyses, comparative genomics as well as for providing training and test sets for predictive algorithms regarding transmembrane β-barrels.
doi:10.1093/nar/gkq863
PMCID: PMC3013764  PMID: 20952406
24.  HHrep: de novo protein repeat detection and the origin of TIM barrels 
Nucleic Acids Research  2006;34(Web Server issue):W137-W142.
HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main strength is its sensitivity, allowing it to detect highly divergent repeat units in protein sequences whose repeats could as yet only be detected from their structures. Examples include sequences with β-propellor fold, ferredoxin-like fold, double psi barrels or (βα)8 (TIM) barrels. We illustrate this with proteins from four superfamilies of TIM barrels by revealing a clear 4- and 8-fold symmetry, which we detect solely from their sequences. This symmetry might be the trace of an ancient origin through duplication of a βαβα or βα unit. HHrep can be accessed at .
doi:10.1093/nar/gkl130
PMCID: PMC1538828  PMID: 16844977
25.  Protein Domain of Unknown Function 3233 is a Translocation Domain of Autotransporter Secretory Mechanism in Gamma proteobacteria 
PLoS ONE  2011;6(11):e25570.
Vibrio cholerae, the enteropathogenic gram negative bacteria is one of the main causative agents of waterborne diseases like cholera. About 1/3rd of the organism's genome is uncharacterised with many protein coding genes lacking structure and functional information. These proteins form significant fraction of the genome and are crucial in understanding the organism's complete functional makeup. In this study we report the general structure and function of a family of hypothetical proteins, Domain of Unknown Function 3233 (DUF3233), which are conserved across gram negative gammaproteobacteria (especially in Vibrio sp. and similar bacteria). Profile and HMM based sequence search methods were used to screen homologues of DUF3233. The I-TASSER fold recognition method was used to build a three dimensional structural model of the domain. The structure resembles the transmembrane beta-barrel with an axial N-terminal helix and twelve antiparallel beta-strands. Using a combination of amphipathy and discrimination analysis we analysed the potential transmembrane beta-barrel forming properties of DUF3233. Sequence, structure and phylogenetic analysis of DUF3233 indicates that this gram negative bacterial hypothetical protein resembles the beta-barrel translocation unit of autotransporter Va secretory mechanism with a gene organisation that differs from the conventional Va system.
doi:10.1371/journal.pone.0025570
PMCID: PMC3206015  PMID: 22073138

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