Evaluation of transmembrane helix predictions in 2014
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Burkhard Rost | Edda Kloppmann | Michael Bernhofer | Jonas Reeb | B. Rost | Michael Bernhofer | Jonas Reeb | Edda Kloppmann
[1] Avner Schlessinger,et al. PredictProtein—an open resource for online prediction of protein structural and functional features , 2014, Nucleic Acids Res..
[2] Kalle Jonasson,et al. Prediction of the human membrane proteome , 2010, Proteomics.
[3] Edgar Jacoby,et al. The 7 TM G‐Protein‐Coupled Receptor Target Family , 2006, ChemMedChem.
[4] Jaime Prilusky,et al. Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology , 2016, Proceedings of the National Academy of Sciences.
[5] G. von Heijne,et al. Prediction of membrane-protein topology from first principles , 2008, Proceedings of the National Academy of Sciences.
[6] B. Rost,et al. TMSEG: Novel prediction of transmembrane helices , 2016, Proteins.
[7] David E. Gloriam,et al. Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse. , 2006, Genomics.
[8] A. Krogh,et al. A combined transmembrane topology and signal peptide prediction method. , 2004, Journal of molecular biology.
[9] S. White. The progress of membrane protein structure determination , 2004, Protein science : a publication of the Protein Society.
[10] Marco Punta,et al. Structural genomics plucks high-hanging membrane proteins. , 2012, Current opinion in structural biology.
[11] Hyeon Joo,et al. OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..
[12] Burkhard Rost,et al. Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming , 1996, ISMB.
[13] Thomas A. Hopf,et al. Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing , 2012, Cell.
[14] C. Peters,et al. Topology Prediction of α-Helical Transmembrane Proteins , 2016 .
[15] Burkhard Rost,et al. UniqueProt: creating representative protein sequence sets , 2003, Nucleic Acids Res..
[16] Shigeki Mitaku,et al. Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces , 2002, Bioinform..
[17] A. Kernytsky,et al. Transmembrane helix predictions revisited , 2002, Protein science : a publication of the Protein Society.
[18] John P. Overington,et al. How many drug targets are there? , 2006, Nature Reviews Drug Discovery.
[19] Masami Ikeda,et al. Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topology , 2001, Silico Biol..
[20] B. Rost,et al. Transmembrane helices predicted at 95% accuracy , 1995, Protein science : a publication of the Protein Society.
[21] Marcin J. Skwark,et al. Sequence analysis SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology , 2008 .
[22] B. Dobberstein,et al. Transfer to proteins across membranes. II. Reconstitution of functional rough microsomes from heterologous components , 1975, The Journal of cell biology.
[23] David W. Burden,et al. Introduction to Proteins , 1995 .
[24] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[25] Marco Punta,et al. Membrane protein prediction methods. , 2007, Methods.
[26] Anders Krogh,et al. Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model , 1998, ISMB.
[27] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[28] Manuel G. Claros,et al. TopPred II: an improved software for membrane protein structure predictions , 1994, Comput. Appl. Biosci..
[29] B. Efron. Nonparametric estimates of standard error: The jackknife, the bootstrap and other methods , 1981 .
[30] G. von Heijne,et al. Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. , 2010, Journal of molecular biology.
[31] Shigeki Mitaku,et al. SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..
[32] D. Baker,et al. Multipass membrane protein structure prediction using Rosetta , 2005, Proteins.
[33] D. Doyle,et al. Transmembrane helix prediction: a comparative evaluation and analysis. , 2005, Protein engineering, design & selection : PEDS.
[34] Frank Alber,et al. Integrating diverse data for structure determination of macromolecular assemblies. , 2008, Annual review of biochemistry.
[35] B. Rost,et al. Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy , 1996, Protein science : a publication of the Protein Society.
[36] G. Vonheijne. The signal peptide. , 1990 .
[37] Zsuzsanna Dosztányi,et al. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank , 2004, Nucleic Acids Res..
[38] Alessandro Vullo,et al. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins , 2006, BMC Bioinformatics.
[39] E. Sonnhammer,et al. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features , 2008, Nucleic acids research.
[40] B. Rost,et al. Comparing function and structure between entire proteomes , 2001, Protein science : a publication of the Protein Society.
[41] Avner Schlessinger,et al. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome , 2013, Nature Structural &Molecular Biology.
[42] N. Grassly,et al. Mathematical models of infectious disease transmission , 2008, Nature Reviews Microbiology.
[43] David T. Jones,et al. Transmembrane protein topology prediction using support vector machines , 2009, BMC Bioinformatics.
[44] Arne Elofsson,et al. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar , 2008, Bioinform..
[45] David T. Jones,et al. Improving the accuracy of transmembrane protein topology prediction using evolutionary information , 2007, Bioinform..
[46] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[47] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[48] István Simon,et al. The HMMTOP transmembrane topology prediction server , 2001, Bioinform..
[49] The UniProt Consortium,et al. Reorganizing the protein space at the Universal Protein Resource (UniProt) , 2011, Nucleic Acids Res..
[50] N. Schenker,et al. Overlapping confidence intervals or standard error intervals: What do they mean in terms of statistical significance? , 2003, Journal of insect science.
[51] Richard A Friesner,et al. An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-em and Evolutionary Data , 2004 .
[52] G. von Heijne,et al. Topogenic signals in integral membrane proteins. , 1988, European journal of biochemistry.
[53] S H White,et al. MPtopo: A database of membrane protein topology , 2001, Protein science : a publication of the Protein Society.
[54] Konstantinos D. Tsirigos,et al. A guideline to proteome‐wide α‐helical membrane protein topology predictions , 2012, Proteomics.
[55] Jeff A. Bilmes,et al. Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks , 2008, PLoS Comput. Biol..
[56] Burkhard Rost,et al. Supporting online material for : LocTree 2 predicts localization for all domains of life , 2012 .
[57] S. Brunak,et al. SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.
[58] Sameer Velankar,et al. E-MSD: an integrated data resource for bioinformatics , 2004, Nucleic Acids Res..
[59] B. Rost. PHD: predicting one-dimensional protein structure by profile-based neural networks. , 1996, Methods in enzymology.
[60] Erik L. L. Sonnhammer,et al. An HMM posterior decoder for sequence feature prediction that includes homology information , 2005, ISMB.
[61] G. von Heijne. The signal peptide. , 1990, The Journal of membrane biology.
[62] T. Stevens,et al. Do more complex organisms have a greater proportion of membrane proteins in their genomes? , 2000, Proteins.
[63] Burkhard Rost,et al. Static benchmarking of membrane helix predictions , 2003, Nucleic Acids Res..
[64] Rolf Apweiler,et al. A collection of well characterised integral membrane proteins , 2000, Bioinform..
[65] G. von Heijne,et al. Membrane protein structure: prediction versus reality. , 2007, Annual review of biochemistry.
[66] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[67] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[68] John D. Westbrook,et al. The Protein Model Portal , 2008, Journal of Structural and Functional Genomics.
[69] Tim Werner,et al. A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions , 2013, BMC Bioinformatics.