Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information.

PubWeight™: 3.40‹?› | Rank: Top 1%

🔗 View Article (PMC 2279939)

Published in Protein Sci on July 01, 2004

Authors

Håkan Viklund1, Arne Elofsson

Author Affiliations

1: Stockholm Bioinformatics Center, Stockholm University, SE-10691 Stockholm, Sweden.

Articles citing this

GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (2010) 6.57

Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics (2009) 4.67

The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93

Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56

TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res (2009) 3.45

Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89

Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55

HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res (2006) 1.82

Hepatitis C virus NS2 protein contributes to virus particle assembly via opposing epistatic interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes. J Virol (2009) 1.76

The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics (2008) 1.69

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet (2014) 1.51

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49

A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci U S A (2006) 1.45

Melanocortin-2 receptor accessory protein MRAP forms antiparallel homodimers. Proc Natl Acad Sci U S A (2007) 1.42

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics (2005) 1.41

Regions of melanocortin 2 (MC2) receptor accessory protein necessary for dual topology and MC2 receptor trafficking and signaling. J Biol Chem (2008) 1.36

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res (2015) 1.35

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29

Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28

Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. Genome Biol (2006) 1.26

Two essential arginine residues in the T components of energy-coupling factor transporters. J Bacteriol (2009) 1.22

APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res (2012) 1.21

Improved membrane protein topology prediction by domain assignments. Protein Sci (2005) 1.16

Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinformatics (2008) 1.15

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Res (2010) 1.13

Structure and function of the melanocortin2 receptor accessory protein (MRAP). Mol Cell Endocrinol (2008) 1.10

CCTOP: a Consensus Constrained TOPology prediction web server. Nucleic Acids Res (2015) 1.06

Structural determinants of skeletal muscle ryanodine receptor gating. J Biol Chem (2013) 1.03

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics (2005) 1.03

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics (2006) 1.01

Investigation of transmembrane proteins using a computational approach. BMC Genomics (2008) 0.98

Rapid membrane protein topology prediction. Bioinformatics (2011) 0.97

Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila. PLoS Biol (2010) 0.96

An automatic method for identifying surface proteins in bacteria: SLEP. BMC Bioinformatics (2010) 0.96

Expediting topology data gathering for the TOPDB database. Nucleic Acids Res (2014) 0.93

APPRIS WebServer and WebServices. Nucleic Acids Res (2015) 0.93

A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. BMC Bioinformatics (2005) 0.92

Comparative mitochondrial genomics within and among species of killifish. BMC Evol Biol (2009) 0.91

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiol (2010) 0.90

Topological and mutational analysis of Saccharomyces cerevisiae Fks1. Eukaryot Cell (2012) 0.88

Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta (2011) 0.88

GO-PROMTO illuminates protein membrane topologies of glycan biosynthetic enzymes in the Golgi apparatus of living tissues. PLoS One (2012) 0.87

The human transmembrane proteome. Biol Direct (2015) 0.87

Characterization of bacterial drug antiporters homologous to mammalian neurotransmitter transporters. J Bacteriol (2005) 0.87

Use of chimeric melanocortin-2 and -4 receptors to identify regions responsible for ligand specificity and dependence on melanocortin 2 receptor accessory protein. Eur J Pharmacol (2011) 0.87

MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics (2009) 0.87

Overexpression of ARGOS Genes Modifies Plant Sensitivity to Ethylene, Leading to Improved Drought Tolerance in Both Arabidopsis and Maize. Plant Physiol (2015) 0.86

Prediction of the burial status of transmembrane residues of helical membrane proteins. BMC Bioinformatics (2007) 0.86

Analysis of an optimal hidden Markov model for secondary structure prediction. BMC Struct Biol (2006) 0.86

Membrane topology of hedgehog acyltransferase. J Biol Chem (2014) 0.86

Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci (2007) 0.85

TOPPER: topology prediction of transmembrane protein based on evidential reasoning. ScientificWorldJournal (2013) 0.85

Alanyl-phosphatidylglycerol and lysyl-phosphatidylglycerol are translocated by the same MprF flippases and have similar capacities to protect against the antibiotic daptomycin in Staphylococcus aureus. Antimicrob Agents Chemother (2012) 0.85

Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter. BMC Microbiol (2009) 0.84

PSPP: a protein structure prediction pipeline for computing clusters. PLoS One (2009) 0.83

Transmembrane protein alignment and fold recognition based on predicted topology. PLoS One (2013) 0.83

Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex. J Biol Chem (2010) 0.83

Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42. BMC Dev Biol (2011) 0.82

Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose. AMB Express (2014) 0.82

Isolation and characterization of a novel haloacid permease from Burkholderia cepacia MBA4. Appl Environ Microbiol (2007) 0.82

Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein. J Biol Chem (2011) 0.80

TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. Bioinformatics (2007) 0.79

Alpha-helical topology prediction and generation of distance restraints in membrane proteins. Biophys J (2008) 0.79

C19orf12 mutation leads to a pallido-pyramidal syndrome. Gene (2013) 0.78

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci (2010) 0.78

DHCR24 associates strongly with the endoplasmic reticulum beyond predicted membrane domains: implications for the activities of this multi-functional enzyme. Biosci Rep (2014) 0.78

A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions. BMC Bioinformatics (2013) 0.78

In silico studies on DARC. Infect Disord Drug Targets (2009) 0.78

Maize and Arabidopsis ARGOS Proteins Interact with Ethylene Receptor Signaling Complex, Supporting a Regulatory Role for ARGOS in Ethylene Signal Transduction. Plant Physiol (2016) 0.78

Calcium-release channels in paramecium. Genomic expansion, differential positioning and partial transcriptional elimination. PLoS One (2011) 0.78

Involvement of PG2212 zinc finger protein in the regulation of oxidative stress resistance in Porphyromonas gingivalis W83. J Bacteriol (2014) 0.78

IgTM: an algorithm to predict transmembrane domains and topology in proteins. BMC Bioinformatics (2008) 0.78

HMM_RA: an improved method for alpha-helical transmembrane protein topology prediction. Bioinform Biol Insights (2008) 0.76

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J (2017) 0.75

Engineered biosynthesis of enduracidin lipoglycopeptide antibiotics using the ramoplanin mannosyltransferase Ram29. Microbiology (2015) 0.75

Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. BMC Genomics (2016) 0.75

How many 3D structures do we need to train a predictor? Genomics Proteomics Bioinformatics (2009) 0.75

Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans. Sci Rep (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Basic local alignment search tool. J Mol Biol (1990) 659.07

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci (1996) 19.74

A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77

Selection of representative protein data sets. Protein Sci (1992) 15.62

The HMMTOP transmembrane topology prediction server. Bioinformatics (2001) 12.57

Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol (1992) 11.97

TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci (1994) 10.03

Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol (1998) 7.72

A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry (1994) 6.64

Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics (2001) 6.53

The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J (1986) 5.48

Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci (1996) 4.58

Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci (1996) 4.50

Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J Mol Biol (1994) 4.07

Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci U S A (1993) 3.92

Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13

Membrane proteins: from sequence to structure. Annu Rev Biophys Biomol Struct (1994) 2.75

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23

Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol (2002) 2.07

MPtopo: A database of membrane protein topology. Protein Sci (2001) 2.04

SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics (2003) 1.66

Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem (2003) 1.40

Reliability of transmembrane predictions in whole-genome data. FEBS Lett (2002) 1.31

Divergent evolution of membrane protein topology: the Escherichia coli RnfA and RnfE homologues. Proc Natl Acad Sci U S A (1999) 1.22

Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci (2003) 1.17

Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci (2002) 1.10

Articles by these authors

3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99

Can correct protein models be identified? Protein Sci (2003) 3.74

TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res (2009) 3.45

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics (2008) 3.20

Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics (2002) 2.66

CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60

Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A (2008) 2.55

Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins (2004) 2.52

Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins (2007) 2.50

Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci (2006) 2.39

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics (2008) 2.38

What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol (2006) 2.27

Domain rearrangements in protein evolution. J Mol Biol (2005) 2.12

All are not equal: a benchmark of different homology modeling programs. Protein Sci (2005) 1.99

Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol (2005) 1.95

Expansion of protein domain repeats. PLoS Comput Biol (2006) 1.93

LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins (2003) 1.90

Arrangements in the modular evolution of proteins. Trends Biochem Sci (2008) 1.78

Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics (2005) 1.71

A study of the membrane-water interface region of membrane proteins. J Mol Biol (2004) 1.68

Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci (2008) 1.56

The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54

Structure is three to ten times more conserved than sequence--a study of structural response in protein cores. Proteins (2009) 1.48

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins (2003) 1.46

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain. Nature (2012) 1.42

Quantification of the elevated rate of domain rearrangements in metazoa. J Mol Biol (2007) 1.39

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29

Pcons.net: protein structure prediction meta server. Nucleic Acids Res (2007) 1.28

Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins (2009) 1.28

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol (2006) 1.27

ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics (2006) 1.24

In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol (2003) 1.21

Preferential attachment in the evolution of metabolic networks. BMC Genomics (2005) 1.20

Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci (2014) 1.13

Identifying and quantifying orphan protein sequences in fungi. J Mol Biol (2009) 1.11

Improved detection of homologous membrane proteins by inclusion of information from topology predictions. Protein Sci (2002) 1.10

PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics (2013) 1.09

Using evolutionary information for the query and target improves fold recognition. Proteins (2004) 1.07

Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J Mol Biol (2009) 1.07

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. Bioinformatics (2012) 1.03

Coils in the membrane core are conserved and functionally important. J Mol Biol (2008) 1.03

Why are polar residues within the membrane core evolutionary conserved? Proteins (2010) 1.02

Tertiary windowing to detect positive diversifying selection. J Mol Evol (2005) 1.01

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biol (2007) 1.00

Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics (2008) 1.00

Repositioning of transmembrane alpha-helices during membrane protein folding. J Mol Biol (2010) 0.97

Nebulin: a study of protein repeat evolution. J Mol Biol (2010) 0.97

Rapid membrane protein topology prediction. Bioinformatics (2011) 0.97

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics (2005) 0.94

Protein expansion is primarily due to indels in intrinsically disordered regions. Mol Biol Evol (2013) 0.94

MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinformatics (2010) 0.90

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (2013) 0.88

The impact of splicing on protein domain architecture. Curr Opin Struct Biol (2013) 0.87

A guideline to proteome-wide α-helical membrane protein topology predictions. Proteomics (2012) 0.86

Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion. J Mol Biol (2012) 0.86

Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci (2007) 0.85

An introduction to membrane proteins. J Proteome Res (2011) 0.85

The evolution of filamin-a protein domain repeat perspective. J Struct Biol (2012) 0.85

Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants. BMC Plant Biol (2010) 0.84

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins. Biochim Biophys Acta (2013) 0.83

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinformatics (2006) 0.81

The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity. Gastroenterology (2011) 0.81

Manipulating the genetic code for membrane protein production: what have we learnt so far? Biochim Biophys Acta (2011) 0.81

Remote homology detection of integral membrane proteins using conserved sequence features. Proteins (2008) 0.81

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. Bioinformatics (2012) 0.79

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein Sci (2010) 0.78

Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins (2014) 0.77

Improved predictions by Pcons.net using multiple templates. Bioinformatics (2010) 0.77

Ligand binding properties of human galanin receptors. Mol Membr Biol (2012) 0.76

KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics (2011) 0.76

Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction. ACS Synth Biol (2015) 0.75

Determining receptor-ligand interaction of human galanin receptor type 3. Neurochem Int (2010) 0.75

Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics (2013) 0.75

The salmon genome (and other issues in bioinformatics). Genome Biol (2002) 0.75

Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods Mol Biol (2013) 0.75