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LocTree3 prediction of localization
2014
Nucleic Acids Research
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The prediction of protein sub-cellular localization is an important step toward elucidating protein function. ...
Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. ...
Interested users may download the LocTree3 De- Reliable predictions more accurate. The reliability index (RI) of LocTree3 relates the strength of a prediction to the performance. ...
doi:10.1093/nar/gku396
pmid:24848019
pmcid:PMC4086075
fatcat:elitvr465zfr5oylrfegv6g4oi
A high-precision hybrid algorithm for predicting eukaryotic protein subcellular localization
[article]
2019
bioRxiv
pre-print
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When tested on Dataset I and Dataset II, BLAST+SWNW showed an average accuracy of 97.18% and 99.60%, respectively, surpassing the performance of other algorithms in predicting eukaryotic protein subcellular ...
E-value Basic Local Alignment Search Tool (BLAST) with the Smith-Waterman (SW) and Needleman-Wunsch (NW) algorithms, and this method has been introduced to predict protein subcellular localization in ...
The prediction of 16 of 24 SLs were 233 better with BLAST+SWNW with an E-value=30 than with LocTree3. ...
doi:10.1101/620179
fatcat:kve5qhmwczcz7iw4old6fekloe
PredictProtein—an open resource for online prediction of protein structural and functional features
2014
Nucleic Acids Research
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(LocTree3), protein-protein binding sites (ISIS2), protein-polynucleotide binding sites (SomeNA) and predictions of the effect of point mu-tations (non-synonymous SNPs) on protein function (SNAP2). ...
The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction ...
New: LocTree3 subcellular localization for all domains of life LocTree3 predicts subcellular localization for proteins in all domains of life (30) . ...
doi:10.1093/nar/gku366
pmid:24799431
pmcid:PMC4086098
fatcat:c5pmgwyx7zg4jjncj4eywixmf4
SCLpred‐MEM : subcellular localization prediction of membrane proteins by Deep N‐to‐1 Convolutional Neural Networks
2021
Proteins: Structure, Function, and Bioinformatics
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Due to the expensive and time-consuming nature of experimental methods of protein subcellular location determination, various computational methods have been developed for subcellular localization prediction ...
matching other state-of-the-art subcellular localization predictors. ...
, 4 contact maps, 5 protein domains, 6 and subcellular localization. 7 Machine learning algorithms are highly successful in protein subcellular localization prediction due to the large volume of ...
doi:10.1002/prot.26144
pmid:33983651
fatcat:qgte7amdjfd3fkggzfnodywrhq
BUSCA: an integrative web server to predict subcellular localization of proteins
2018
Nucleic Acids Research
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We propose BUSCA as an integrated and accurate resource for the annotation of protein subcellular localization. ...
Here, we present BUSCA (http://busca.biocomp. unibo.it), a novel web server that integrates different computational tools for predicting protein subcellular localization. ...
LocTree3). ...
doi:10.1093/nar/gky320
pmid:29718411
pmcid:PMC6031068
fatcat:cninzcq2fzhilec3qjaixgrori
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species
2021
Journal of Molecular Evolution
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AbstractThe native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. ...
The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47–62% of all proteins, while 7–21% of the proteins were predicted in the plasma membrane and 4–15% to ...
C The PCA adds more details to the comparison between species from the LocTree3 predictions. ...
doi:10.1007/s00239-021-10022-4
pmid:34328525
pmcid:PMC8379119
fatcat:xwonpgdac5cm7dyv6dalz7svmq
PSO-LocBact: A Consensus Method for Optimizing Multiple Classifier Results for Predicting the Subcellular Localization of Bacterial Proteins
2019
BioMed Research International
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with the aim of integrating diverse prediction models to enhance the final predictions. ...
Hence, to address this issue, this work proposes the use of the particle swarm optimization (PSO) algorithm to combine the prediction outputs from multiple different subcellular localization predictors ...
Acknowledgments Sirapop Nuannimnoi was supported by Food Innopolis Grant P-17-50583. e authors acknowledge the use of a computing facility provided by King Mongkut's University of Technology onburi through ...
doi:10.1155/2019/5617153
pmid:31886228
pmcid:PMC6925685
fatcat:wvtgmi6us5hchbg3ytif5bq66y
Exploring Realm of Proteases of Leishmania donovani Genome and Gene Expression Analysis of Proteases under Apoptotic Condition
2016
Journal of Proteomics & Bioinformatics
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Financial support by Department of Biotechnology, Government of India in the form of research grants (Project no: BT/01/IYBA/2009) to VKD is also acknowledged. ...
Disclosure Statement No potential conflict of interest was reported by the authors. ...
LocTree3 does not predict the multiple sub-cellular localization of signal peptidase; hence it became important to use another sub-cellular localization prediction tool which may predict multiple localization ...
doi:10.4172/jpb.1000407
fatcat:oiwda4ziibgr5davbm3hcbdy3u
ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling
2015
Nucleic Acids Research
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Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein-protein interactions, membrane spanning regions and protein domains. ...
three domains of life. ...
ACKNOWLEDGEMENTS Thanks to Thomas Rattei and the SIMAP initiative for providing the similarity matrix data and the LocTree3 team for providing subcellular localization data. ...
doi:10.1093/nar/gkv455
pmid:25956654
pmcid:PMC4489284
fatcat:ifwzhjf5zrhshjiu34ar6x3txi
Spectrum of protein localization in proteomes captures evolutionary relation between species
[article]
2019
bioRxiv
pre-print
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The native subcellular localization or cellular compartment of a protein is the one in which it acts most often; it is one aspect of protein function. ...
To gauge the bias of prediction methods, we merged all available experimental annotations for the human proteome. ...
Predictions of the location spectra for ten completely sequenced model eukaryotes in seven main localization classes were computed by LocTree3 (Fig. 3 , SOM: Table S2 ). ...
doi:10.1101/845362
fatcat:liexltllpjfj3iuuocro2b6szi
Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer
2020
ACS Omega
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Although evidences have established the involvement of E. coli in the growth of colon cancer, the molecular mechanisms of carcinogenesis of cancer growth and development are not well understood. ...
The results of the current in silico study provide insights into E. coli pathogenesis and may aid in designing new preventive and therapeutic strategies. ...
■ ACKNOWLEDGMENTS The authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding this work through research group no (RG-1440-059). ...
doi:10.1021/acsomega.9b04042
pmid:32280866
pmcid:PMC7143404
fatcat:fd2tik3xmnhuxhvr3lrnl32ye4
Benchmarking subcellular localization and variant tolerance predictors on membrane proteins
2019
BMC Genomics
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A large number of prediction methods have been introduced to predict protein subcellular localization as well as the tolerance or pathogenicity of amino acid substitutions. ...
Further, we tested with the high quality dataset also the performance of seven subcellular localization predictors on membrane proteins. ...
About this supplement This article has been published as part of BMC Genomics Volume 20 Supplement 8, 2019: Proceedings of VarI-COSI 2018: identification and annotation of genetic variants in the context ...
doi:10.1186/s12864-019-5865-0
pmid:31307390
pmcid:PMC6631444
fatcat:m5pihglyyfdkhf2yvr5pdpgfky
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting
2020
Briefings in Bioinformatics
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Novelty elements include improved cell-wall protein prediction, including differentiation of the type of interaction, prediction of non-canonical secretion pathway target proteins, separate prediction ...
However, the experimental determination of protein localization is time consuming and expensive. Therefore, various localization predictors have been developed for particular groups of species. ...
Acknowledgments We would like to thank the developers of all prediction tools mentioned in this paper. Without the software they developed, the presented GP 4 tool could not exist. ...
doi:10.1093/bib/bbaa302
pmid:33227814
pmcid:PMC8294519
fatcat:al246yh2gngixj7ebbaeuqehru
Structural Prediction and Mutational Analysis of Rv3906c Gene of Mycobacterium tuberculosis H37Rv to Determine Its Essentiality in Survival
2018
Advances in Bioinformatics
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This gene shows interaction with its adjacent genes as well as pcnA which is a polymerase and localized in the extracellular region and found to be a soluble protein. ...
Stress conditions like pH and temperature also change stability of the protein. A decrease in stability at this position might play a role in inhibition of survival of the pathogen. ...
Acknowledgments The authors acknowledge financial support from the Department of Science and Technology-SERB, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology ...
doi:10.1155/2018/6152014
pmid:30186322
pmcid:PMC6114228
fatcat:i2bd4zcesvgotbc7zdddzbr3vq
SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks
2020
Bioinformatics
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We introduce SCLpred-EMS a subcellular localization predictor powered by an ensemble of Deep N-to-1 Convolutional Neural Networks. ...
Motivation The subcellular location of a protein can provide useful information for protein function prediction and drug design. ...
Acknowledgements The authors acknowledge contributions of Amina Khalid and Tejaswini Kumar to the collection of the preliminary benchmarking results and the Research IT Service at University College Dublin ...
doi:10.1093/bioinformatics/btaa156
pmid:32142105
fatcat:v2pkc3t3dzh75jsvgji2lqw7my
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