ArticlePloS one2012
ApicoAP: the first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 56 citations in OpenAlex.
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- Decoding the Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance.Journal of molecular biology · 2025Article
- tRNA modifying enzymes MnmE and MnmG are essential forbioRxiv : the preprint server for biology · 2025Article
- CRISPR screens identify genes essential formBio · 2024Article
- Comparative chemical genomics inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Directing traffic: Chaperone-mediated protein transport in malaria parasites.Cellular microbiology · 2020Review
- Plastid biogenesis in malaria parasites requires the interactions and catalytic activity of the Clp proteolytic system.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A mevalonate bypass system facilitates elucidation of plastid biology in malaria parasites.PLoS pathogens · 2020Article
- Article
- ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors.Database : the journal of biological databases and curation · 2019Article
- Article
- Prediction of Signal Peptides in Proteins from Malaria Parasites.International journal of molecular sciences · 2018Article
- Heterologous expression inFEBS open bio · 2018Article
- Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites.PLoS biology · 2018Article
- Article
- Genomics of apicomplexan parasites.Critical reviews in biochemistry and molecular biology · 2017Review
- Two phylogenetically and compartmentally distinct CDP-diacylglycerol synthases cooperate for lipid biogenesis inThe Journal of biological chemistry · 2017Article
- Characterization of HSP90 isoforms in transformed bovine leukocytes infected with Theileria annulata.Cellular microbiology · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMost of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for the survival of the parasite, but its unique properties make it an ideal drug target. The majority of apicoplast-associated proteins are nuclear encoded and targeted post-translationally to the organellar lumen via a bipartite signaling mechanism that requires an N-terminal signal and transit peptide (TP). Attempts to define a consensus motif that universally identifies apicoplast TPs have failed. METHODOLOGY/PRINCIPAL
findingsIn this study, we propose a generalized rule-based classification model to identify apicoplast-targeted proteins (ApicoTPs) that use a bipartite signaling mechanism. Given a training set specific to an organism, this model, called ApicoAP, incorporates a procedure based on a genetic algorithm to tailor a discriminating rule that exploits the known characteristics of ApicoTPs. Performance of ApicoAP is evaluated for four labeled datasets of Plasmodium falciparum, Plasmodium yoelii, Babesia bovis, and Toxoplasma gondii proteins. ApicoAP improves the classification accuracy of the published dataset for P. falciparum to 94%, originally 90% using PlasmoAP. CONCLUSIONS/SIGNIFICANCE: We present a parametric model for ApicoTPs and a procedure to optimize the model parameters for a given training set. A major asset of this model is that it is customizable to different parasite genomes. The ApicoAP prediction software is available at http://code.google.com/p/apicoap/ and http://bcb.eecs.wsu.edu.
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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.