ArticleJournal of structural and functional genomics2009
Structural genomics target selection for the New York consortium on membrane protein structure.
Article in Journal of structural and functional genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- UniTmp: unified resources for transmembrane proteins.Nucleic acids research · 2024Article
- How AlphaFold2 shaped the structural coverage of the human transmembrane proteome.Scientific reports · 2023Article
- Article
- High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics.Protein science : a publication of the Protein Society · 2022Article
- Fine Sampling of Sequence Space for Membrane Protein Structural Biology.Journal of molecular biology · 2021Article
- Article
- Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon.Journal of the American Chemical Society · 2020Review
- Article
- A statistical model for improved membrane protein expression using sequence-derived features.The Journal of biological chemistry · 2018Article
- Prediction of protein disorder based on IUPred.Protein science : a publication of the Protein Society · 2018Article
- Structural basis for conductance through TRIC cation channels.Nature communications · 2017Article
- TSTMP: target selection for structural genomics of human transmembrane proteins.Nucleic acids research · 2017Article
- TMSEG: Novel prediction of transmembrane helices.Proteins · 2016Article
- Unexpected features of the dark proteome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A critical evaluation of in silico methods for detection of membrane protein intrinsic disorder.Biophysical journal · 2014Article
- Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- High-throughput cloning and expression of integral membrane proteins in Escherichia coli.Current protocols in protein science · 2013Article
- Coordinating the impact of structural genomics on the human α-helical transmembrane proteome.Nature structural & molecular biology · 2013Article
- Structural genomics plucks high-hanging membrane proteins.Current opinion in structural biology · 2012Review
- Computational approaches to selecting and optimising targets for structural biology.Methods (San Diego, Calif.) · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at least two predicted transmembrane helices, no predicted long disordered regions and, except for community nominated targets, no significant sequence similarity in the predicted transmembrane region to any known protein structure. Proteins that feed our experimental pipeline are selected by defining a protein seed and searching the set of all valid targets for proteins that are likely to have a transmembrane region structurally similar to that of the seed. We require sequence similarity aligning at least half of the predicted transmembrane region of seed and target. Seeds are selected according to their feasibility and/or biological interest, and they include both centrally selected targets and community nominated targets. As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space.
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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.