ArticleNucleic acids research2012
Transmembrane helix: simple or complex.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- The Pentameric Ligand-Gated Ion Channel Family: A New Member of the Voltage Gated Ion Channel Superfamily?International journal of molecular sciences · 2024Article
- Computational approaches for molecular characterization and structure-based functional elucidation of a hypothetical protein from Mycobacterium tuberculosis.Genomics & informatics · 2023Article
- Sequence Similarity among Structural Repeats in the Piezo Family of Mechanosensitive Ion Channels.Microbial physiology · 2023Article
- Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily.Microbial physiology · 2022Article
- Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.Biology direct · 2021Article
- Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes.Biochimica et biophysica acta. Biomembranes · 2020Article
- Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families.PloS one · 2020Article
- Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z.Cell cycle (Georgetown, Tex.) · 2018Article
- Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".BMC biology · 2017Article
- xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation.Biology direct · 2016Article
- Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.PLoS computational biology · 2015Article
- On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation.BMC bioinformatics · 2014Article
- Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins.Journal of virology · 2014Article
- Transamidase subunit GAA1/GPAA1 is a M28 family metallo-peptide-synthetase that catalyzes the peptide bond formation between the substrate protein's omega-site and the GPI lipid anchor's phosphoethanolamine.Cell cycle (Georgetown, Tex.) · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transmembrane helical segments (TMs) can be classified into two groups of so-called 'simple' and 'complex' TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely accessible at http://tmsoc.bii.a-star.edu.sg or available for download.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.