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LocTree3 prediction of localization

Tatyana Goldberg, Maximilian Hecht, Tobias Hamp, Timothy Karl, Guy Yachdav, Nadeem Ahmed, Uwe Altermann, Philipp Angerer, Sonja Ansorge, Kinga Balasz, Michael Bernhofer, Alexander Betz (+22 others)
2014 Nucleic Acids Research  
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]

Dahan Zhang, Haiyun Huang, Xiaogang Bai, Xiaodong Fang, Yi Zhang
2019 bioRxiv   pre-print
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

Guy Yachdav, Edda Kloppmann, Laszlo Kajan, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy (+8 others)
2014 Nucleic Acids Research  
(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

Manaz Kaleel, Liam Ellinger, Clodagh Lalor, Gianluca Pollastri, Catherine Mooney
2021 Proteins: Structure, Function, and Bioinformatics  
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

Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio
2018 Nucleic Acids Research  
We propose BUSCA as an integrated and accurate resource for the annotation of protein subcellular localization.  ...  Here, we present BUSCA (http://busca.biocomp., 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

Valérie Marot-Lassauzaie, Tatyana Goldberg, Jose Juan Almagro Armenteros, Henrik Nielsen, Burkhard Rost
2021 Journal of Molecular Evolution  
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

Supatcha Lertampaiporn, Sirapop Nuannimnoi, Tayvich Vorapreeda, Nipa Chokesajjawatee, Wonnop Visessanguan, Chinae Thammarongtham
2019 BioMed Research International  
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

Ritesh Kumar, Pratyajit Mohapatra
2016 Journal of Proteomics & Bioinformatics  
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

Yiming Cheng, Fabiana Perocchi
2015 Nucleic Acids Research  
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]

Valerie Marot-Lassauzaie, Tatyana Goldberg, Burkhard Rost
2019 bioRxiv   pre-print
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

Shahanavaj Khan, Sabika Zaidi, Abdulaziz Saleh Alouffi, Iftekhar Hassan, Ahmad Imran, Rais Ahmad Khan
2020 ACS Omega  
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

Tommaso Orioli, Mauno Vihinen
2019 BMC Genomics  
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

Stefano Grasso, Tjeerd van Rij, Jan Maarten van Dijl
2020 Briefings in Bioinformatics  
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

Md. Amjad Beg, Shivangi, Sonu Chand Thakur, Laxman S. Meena
2018 Advances in Bioinformatics  
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

Manaz Kaleel, Yandan Zheng, Jialiang Chen, Xuanming Feng, Jeremy C Simpson, Gianluca Pollastri, Catherine Mooney, Pier Luigi Martelli
2020 Bioinformatics  
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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