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Detailed prediction of protein sub-nuclear localization

Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2019 BMC Bioinformatics  
Sub-nuclear structures or locations are associated with various nuclear processes. Proteins localized in these substructures are important to understand the interior nuclear mechanisms.  ...  A Gene Ontology (GO) analysis of the enrichment of biological processes revealed that the predicted sub-nuclear compartments matched the expected functionality.  ...  ML refined the existing implementation, performed GO enrichment analysis and analysis of protein-protein interactions for nuclear proteins and did the major part of writing the manuscript.  ... 
doi:10.1186/s12859-019-2790-9 pmid:31014229 pmcid:PMC6480651 fatcat:l6nkndl4tjhovpzj4cywqq3pvy

Correction to: Detailed prediction of protein sub-nuclear localization

Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2019 BMC Bioinformatics  
Following publication of the original article [1], the author reported that an incorrect figure has been published as Figure 2. The correct Figure 2 is shown below.  ...  13 nuclear sub-structures, 19% of all proteins were predicted at RI > 60 (point marked by dotted lines).  ...  For our data set, RI < 20 did not correlate with accuracy. b For the prediction of traveler proteins, 29% of all proteins were predicted at RI > 60 (part B, point marked by dotted lines) with Q2 = 78%  ... 
doi:10.1186/s12859-019-3305-4 pmid:31861997 pmcid:PMC6925513 fatcat:ilov2jm73rgyncgc3axzsg4k3e

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets

R. Nair, B. Rost
2004 Nucleic Acids Research  
The web server can be used to predict sub-cellular localization of proteins from their amino acid sequence.  ...  LOCtarget predicts localization through a combination of four different methods: known nuclear localization signals (PredictNLS), homology-based transfer of experimental annotations (LOChom), inference  ...  The work of R.N. and B.R. was supported by the grant DBI-0131168 from the National Science Foundation (NSF) and the grant R01-LM07329-01 from the National Library of Medicine (NLM).  ... 
doi:10.1093/nar/gkh441 pmid:15215440 pmcid:PMC441579 fatcat:77gxe5nz4fgsljdohhtfpo4ery

LOC3D: annotate sub-cellular localization for protein structures

R. Nair
2003 Nucleic Acids Research  
Localization is predicted using four different methods: (i) PredictNLS, prediction of nuclear proteins through nuclear localization signals; (ii) LOChom, inferring localization through sequence homology  ...  LOC3D (http://cubic.bioc.columbia.edu/db/LOC3d/) is both a weekly-updated database and a web server for predictions of sub-cellular localization for eukaryotic proteins of known three-dimensional (3D)  ...  The work of R.N. and B.R. was supported by grant DBI-0131168 from the National Science Foundation (NSF).  ... 
doi:10.1093/nar/gkg514 pmid:12824321 pmcid:PMC168921 fatcat:tzrv267iaffinb2cpckvofi3w4

Protein Sub-Nuclear Localization Prediction Using SVM and Pfam Domain Information

Ravindra Kumar, Sohni Jain, Bandana Kumari, Manish Kumar, Gajendra P. S. Raghava
2014 PLoS ONE  
Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins.  ...  A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at  ...  We also wish to thank the two anonymous reviewers whose constructive comments were very helpful in strengthening the presentation of this paper. Author Contributions  ... 
doi:10.1371/journal.pone.0098345 pmid:24897370 pmcid:PMC4045734 fatcat:2zwaukse5na6phjpy67whxqx2u

Prelocabc: A Novel Predictor of Protein Sub-cellular Localization Using a Bayesian Classifier

Yanqiong Zhang
2011 Journal of Proteomics & Bioinformatics  
Details of the characteristics of the existing predictors for protein sub-cellular localization have been summarized in Supporting materials\supplement.doc\Table S1.  ...  Users may submit their protein sequences online, and the prediction results for protein sub-cellular localization will be returned.  ...  We thank Xiaohong Qian, Wantao Ying, Songfeng Wu, Yunwei Hao, Aihua Sun and Lin Hou in Beijing Proteome Research Center for their helpful discussion; our IT Engineer Yi Liu for publishing the online predicting  ... 
doi:10.4172/jpb.1000165 fatcat:rkzqd2wahngwbhbarizaudrlda

Inferring sub-cellular localization through automated lexical analysis

R. Nair, B. Rost
2002 Bioinformatics  
In contrast, information about the sub-cellular localization is available for only a few proteins. Experts can often infer localization from keywords describing protein function.  ...  LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes. Availability: Annotations of localization for eukaryotes at:  ...  The work was supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health.  ... 
doi:10.1093/bioinformatics/18.suppl_1.s78 pmid:12169534 fatcat:i2aw3n56vjddrgck2h5x5a633y

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA

Shunfang Wang, Shuhui Liu
2015 International Journal of Molecular Sciences  
An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization.  ...  representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one.  ...  Acknowledgments: This research is fully supported by grants from National Natural Science Foundation of China (11261068, 11171293).  ... 
doi:10.3390/ijms161226237 pmid:26703574 pmcid:PMC4691178 fatcat:26kksr4wgfcpvoq6ughtftycwu

Systems Biology Approaches for the Prediction of Possible Role of Chlamydia pneumoniae Proteins in the Etiology of Lung Cancer

Shahanavaj Khan, Ahamad Imran, Abdul Arif Khan, Mohd Abul Kalam, Aws Alshamsan, Carl G. Maki
2016 PLoS ONE  
The current study was performed for the prediction of nuclear targeting protein of C. pneumoniae in the host cell using bioinformatics predictors including ExPASy pI/Mw tool, nuclear localization signal  ...  (NLS) mapper, balanced sub cellular localization predictor (BaCeILo), and Hum-mPLoc 2.0.  ...  BaCeILo predict five classes of sub cellular localization including nuclear, mitochondrial, cytoplasmic, secretory, and chloroplast.  ... 
doi:10.1371/journal.pone.0148530 pmid:26871581 pmcid:PMC4752481 fatcat:ch4ohnb36bfbpjgn24qvxqeev4

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

Fanchi Meng, Insung Na, Lukasz Kurgan, Vladimir Uversky
2015 International Journal of Molecular Sciences  
We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina  ...  Therefore, our work provides support to the idea of the functional importance of intrinsic disorder in the cell nucleus and shows that many proteins associated with sub-nuclear organelles in nuclei of  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms17010024 pmid:26712748 pmcid:PMC4730271 fatcat:kkbizttrtfdsdibr4dwimhydou

Prediction of Sub-cellular Localization of Scramblase Protein Family

Babita Sahoo, Santosh Kumar Sahu, Tripti Swarnkar
2010 International journal of computer and communication technology  
In the present work, we discuss an anaysis about the localization of different members of scramblase protein family.  ...  Different scramblase sequences were picked up from organisms of all eukaryotic phyla and their localization were predicted using the P-SORT programme.  ...  To get further insight into the localization of various members of scramblase proteins across differerent phyla, we performed a prediction of sub-cellular locations of there proteins using the P-SORT program  ... 
doi:10.47893/ijcct.2010.1043 fatcat:ve4ujih6znfd3aoqfqld7pyvym

Determination of the Pseudo-Atomic Structure of Nuclear Pore Complex (NPC) Components by Small Angle X-Ray Scattering (SAXS) and Computational Modeling

Seung Joong Kim, Jeremy Phillips, Anne Martel, Dina Schneidman, Michael Sauder, Michael P. Rout, Hiro Tsuruta, Andrej Sali
2010 Biophysical Journal  
De novo prediction of the protein structure, modeling the native structure of a protein from its sequence information when homologous protein structures are not available from the database, is one of the  ...  We specifically focus on components of two sub-complexes, the 7-protein Nup84 sub-complex, and the 4-protein Nup170 sub-complex, for which complementary experimental data are available.  ...  of these sub-complexes and proteins by simultaneously minimizing violations of all of the restraints.  ... 
doi:10.1016/j.bpj.2009.12.2506 fatcat:nsxple3rrzgwhabgsobetpdqte

Better prediction of sub-cellular localization by combining evolutionary and structural information

Rajesh Nair, Burkhard Rost
2003 Proteins: Structure, Function, and Bioinformatics  
The native sub-cellular compartment of a protein is one aspect of its function. Thus, predicting localization is an important step toward predicting function.  ...  The amino acid composition of a protein correlates with its localization. All general prediction methods employed this observation.  ...  of nuclear proteins through nuclear localization signals; 22, 75 HSSP, database of protein structuresequence alignments; 61 NNPSL, neural networks predicting localization; 31 NLS, nuclear localization  ... 
doi:10.1002/prot.10507 pmid:14635133 fatcat:vhwfh7izzram5ppsbu545fkiky

PREDICTING NUCLEOLAR PROTEINS USING SUPPORT-VECTOR MACHINES

MIKAEL BODÉN
2007 Proceedings of the 6th Asia-Pacific Bioinformatics Conference  
The intra-nuclear organisation of proteins is based on possibly transient interactions with morphologically defined compartments like the nucleolus.  ...  The fluidity of trafficking challenges the development of models that accurately identify compartment membership for novel proteins.  ...  Acknowledgments This work was supported by the ARC Centre of Complex Systems. Lynne Davis and Johnson Shih both contributed to this paper by implementing some of the kernels.  ... 
doi:10.1142/9781848161092_0005 fatcat:6ez7sed45zgh3jecnkyw3vykaq

SChloro: directingViridiplantaeproteins to six chloroplastic sub-compartments

Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2016 Bioinformatics  
Given the relation between protein function and localization, the availability of effective computational tools to predict protein sub-organelle localizations is crucial for large-scale functional studies  ...  Results: In this paper we present SChloro, a novel machine-learning approach to predict protein subchloroplastic localization, based on targeting signal detection and membrane protein information.  ...  However, the prediction of more de-tailed sub-localizations, such as the different sub-chloroplastic compartments, is challenging considering the paucity of detailed experimental annotations in publicly  ... 
doi:10.1093/bioinformatics/btw656 pmid:28172591 pmcid:PMC5408801 fatcat:nm6l4m3ayjaj5bfpmy46joh3lu
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