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Frequent-subsequence-based prediction of outer membrane proteins

Rong She, Fei Chen, Ke Wang, Martin Ester, Jennifer L. Gardy, Fiona S. L. Brinkman
2003 Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '03  
Proteins resident in this membrane (outer membrane proteins, or OMPs) are of primary research interest for antibiotic and vaccine drug design as they are on the surface of the bacteria and so are the most  ...  In this paper, we present two methods to identify OMPs based on frequent subsequences and test them on all Gramnegative bacterial proteins whose localizations have been determined by biological experiments  ...  Martelli (University of Bologna, Italy) for his valuable support in running his OMP prediction algorithm on our dataset and providing us with the classification results. We also thank C.  ... 
doi:10.1145/956750.956800 dblp:conf/kdd/SheCWEGB03 fatcat:zuzk6uofnrel5elltvuox6rmca

Frequent-subsequence-based prediction of outer membrane proteins

Rong She, Fei Chen, Ke Wang, Martin Ester, Jennifer L. Gardy, Fiona S. L. Brinkman
2003 Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '03  
Proteins resident in this membrane (outer membrane proteins, or OMPs) are of primary research interest for antibiotic and vaccine drug design as they are on the surface of the bacteria and so are the most  ...  In this paper, we present two methods to identify OMPs based on frequent subsequences and test them on all Gramnegative bacterial proteins whose localizations have been determined by biological experiments  ...  Martelli (University of Bologna, Italy) for his valuable support in running his OMP prediction algorithm on our dataset and providing us with the classification results. We also thank C.  ... 
doi:10.1145/956790.956800 fatcat:ag4e6gth6rgxbhtwcgvkt7o4xq

Frequent Subsequence-Based Protein Localization [chapter]

Osmar R. Zaïane, Yang Wang, Randy Goebel, Gregory Taylor
2006 Lecture Notes in Computer Science  
In this paper, we present three methods using frequent subsequences of amino acids: one based on support vector machines (SVM), one based on boosting and FSP, a new frequent subsequence pattern method.  ...  Insofar as these proteins are strategically positioned to play a role in resistance to environmental stress, biologists are interested in proteomic tools in analyzing extracellular proteins.  ...  [22] proposed some methods for outer membrane protein classification based on frequent subsequences.  ... 
doi:10.1007/11691730_5 fatcat:ksyshvqguzhrrblo6xzz24zuu4

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster, Fiona S. L. Brinkman
2010 Computer applications in the biosciences : CABIOS  
However, the recall needs to be improved and no accurate SCL predictors yet make predictions for Archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell  ...  Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program.  ...  ACKNOWLEDGEMENTS The authors would like to thank Francis Lim for protein sample processing for mass spectrometry analysis, as well as Kurt McMillan and Yifeng Liu for providing PA 3.0 whole genome prediction  ... 
doi:10.1093/bioinformatics/btq249 pmid:20472543 pmcid:PMC2887053 fatcat:2xak454utjf3xbm55harjgtntm

PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

J. L. Gardy, M. R. Laird, F. Chen, S. Rey, C. J. Walsh, M. Ester, F. S. L. Brinkman
2004 Bioinformatics  
Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0.  ...  We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size.  ...  Department of Computing Science.  ... 
doi:10.1093/bioinformatics/bti057 pmid:15501914 fatcat:wpkhw5qocnhdjp7xcvzh5oxfai

Genome-wide protein localization prediction strategies for gram negative bacteria

Margaret F Romine
2011 BMC Genomics  
Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function.  ...  Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved  ...  subsequent sequence identification by gel-free mass spectrometric-based methods for global characterization of proteins.  ... 
doi:10.1186/1471-2164-12-s1-s1 pmid:21810203 pmcid:PMC3223724 fatcat:iltyd7ceyjdohaqrbglaocikta

Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae

Eva Heinz, Patrick Tischler, Thomas Rattei, Garry Myers, Michael Wagner, Matthias Horn
2009 BMC Genomics  
We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria.  ...  outer membrane protein composition.  ...  Sequencing of P. acanthamoebae was accomplished with support from the United States National Institute of Health (NIH).  ... 
doi:10.1186/1471-2164-10-634 pmid:20040079 pmcid:PMC2811131 fatcat:u2p2ogdbsbcq3gaazbdg2yjjau

PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea

N. Y. Yu, M. R. Laird, C. Spencer, F. S. L. Brinkman
2010 Nucleic Acids Research  
The first version of PSORTdb provided a valuable resource comprising a data set of proteins of known SCL (ePSORTdb) as well as pre-computed SCL predictions for proteomes derived from complete bacterial  ...  This updating approach uses a novel sequence analysis we developed that detects whether the microbe being analyzed has an outer membrane.  ...  ACKNOWLEDGEMENTS We thank NCBI for providing a compilation of complete microbial genomes data and gratefully acknowledge Raymond Lo for comments regarding this article.  ... 
doi:10.1093/nar/gkq1093 pmid:21071402 pmcid:PMC3013690 fatcat:76gzfw4bszenzdxd2qitzi6peu

Towards a peptide-based vaccine against Shigella sonnei : A subtractive reverse vaccinology based approach

Shehneela Baseer, Sajjad Ahmad, Kara E. Ranaghan, Syed Sikander Azam
2017 Biologicals (Print)  
Towards a peptide-based vaccine against Shigella sonnei: A subtractive reverse vaccinology based approach. Biologicals.  ...  (LpfC), Putative outer membrane porin protein (nmpC), Porin protein, Phophoporin protein E (PhoE), Outer membrane protein E, Outer membrane protein C (OmpC), Outer membrane protein F (OmpF), membrane  ...  The blast screen identified fourteen proteins: Cation transporter, E3 ubiquitin--protein ligase, outer membrane protein (TolC), major curlin subunit protein, Outer membrane protein A (OmpA), fimbrial protein  ... 
doi:10.1016/j.biologicals.2017.08.004 pmid:28826780 fatcat:yfm4nwmifzbqtdms2kidd6tkdm

Identification of uropathogenic Escherichia coli surface proteins by shotgun proteomics

Matthew S. Walters, Harry L.T. Mobley
2009 Journal of Microbiological Methods  
Nine of the 25 predicted outer membrane proteins were part of iron transport systems or putative iron-regulated virulence proteins, indicating the importance of iron acquisition during growth in urine.  ...  This method discovered 25 predicted outer membrane proteins expressed by UPEC while growing in human urine.  ...  Acknowledgments Proteomics data were provided by the Michigan Proteome Consortium (http://www.proteomeconsortium.org), which is supported in part by funds from the Michigan Life Sciences Corridor (State of  ... 
doi:10.1016/j.mimet.2009.04.013 pmid:19426766 pmcid:PMC2713358 fatcat:2lzyanrvujbe5ar5pjeiqnct3i

Immuno-informatics driven proteome-wide investigation revealed novel peptide-based vaccine targets against emerging multiple drug resistant Providencia stuartii

Yelda Asad, Sajjad Ahmad, Thanyada Rungrotmongkol, Kara E. Ranaghan, Syed Sikander Azam
2018 Journal of Molecular Graphics and Modelling  
KEGG Name A0A140STA8 Outer membrane usher protein FimD1 A0A140NFQ5 Outer membrane usher protein FimD2 A0A140NKU8 Outer membrane usher protein FimD3 A0A140STH0 Outer membrane usher protein  ...  FimD4 A0A140NJK0 Outer membrane usher protein FimD5 A0A140NPZ6 Outer membrane usher protein FimD6 A0A140NJ67 Outer membrane usher protein FimD7 A0A140NNX3 Outer membrane usher protein  ... 
doi:10.1016/j.jmgm.2018.01.010 pmid:29414043 fatcat:e4wdvldetjaxvbq6ghd5logbai

Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria

Sébastien Rey, Jennifer L Gardy, Fiona S L Brinkman
2005 BMC Genomics  
PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined  ...  By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes.  ...  Laird for their work in the development of PSORTdb and PSORTb, as well as Raymond Lo for his critical reading of the manuscript. SR is a Swiss National Science Foundation Scholar.  ... 
doi:10.1186/1471-2164-6-162 pmid:16288665 pmcid:PMC1314894 fatcat:fmrxlowunrdblbakwwtzo2cyca

Prediction of Epitopes in the Proteome of Helicobacter pylori

Elkin Navarro-Quiroz, Roberto Navarro-Quiroz, Pierine España-Puccini, José Luis Villarreal, Anderson Díaz Perez, Cecilia Fernandez Ponce, Jorge Bilbao, Lucy Vasquez, Dary Luz Mendoza
2018 Global Journal of Health Science  
Twenty-two external membrane proteins from H. pylori Strain 26695 (accession number NC_000915) were identified using the web tool Vaxign (http://www.violinet.org/vaxign/).  ...  in H. pylori proteins.  ...  NP_207516.1 Outer Membrane 0.653 NP_207519.1 Outer Membrane 0.640 NP_207575.1 Outer Membrane 0.517 Table 3 . 3 Predicted epitopes for MHC I in proteins of Helicobacter pylori.  ... 
doi:10.5539/gjhs.v10n7p148 fatcat:akhrp7omhvah3mhyveizuma3bq

Reverse vaccinology approach for the identification and characterization of outer membrane proteins of Shigella flexneri as potential cellular- and antibody-dependent vaccine candidates

Chiuan Yee Leow, Ada Kazi, Che Muhammad Khairul Hisyam Ismail, Candy Chuah, Boon Huat Lim, Chiuan Herng Leow, Kirnpal Kaur Banga Singh
2020 Clinical and experimental vaccine research  
In this study, a reverse vaccinology approach was employed to identify most conserved and immunogenic outer membrane proteins (OMPs) of S. flexneri 2a.  ...  Protein-protein interactions analysis using STRING software (https://string-db.org/) revealed that five of these OMPs may potentially interact with other intracellular proteins which are involved in beta-lactam  ...  Outer membrane receptor (fepA), outer membrane porin protein C (ompC), lipoprotein NlpD (nlpD_1), outer membrane channel protein (tolC), and lipoprotein (nlpD_2) were predicted consisting of N-terminal  ... 
doi:10.7774/cevr.2020.9.1.15 pmid:32095437 pmcid:PMC7024733 fatcat:tdio7yqq2rggni4eov4i724ju4

Use of Pseudomonas putida EstA as an Anchoring Motif for Display of a Periplasmic Enzyme on the Surface of Escherichia coli

T. H. Yang, J. G. Pan, Y. S. Seo, J. S. Rhee
2004 Applied and Environmental Microbiology  
The investigation of growth kinetics and host cell viability showed that the presence of the EstA translocator domain in the outer membrane neither inhibits cell growth nor affects cell viability.  ...  membrane esterase (EstA), which is a member of the lipolytic autotransporter enzymes.  ...  outer membrane.  ... 
doi:10.1128/aem.70.12.6968-6976.2004 pmid:15574889 pmcid:PMC535197 fatcat:cmvg2s4qx5dkvafeu6q4vkjsja
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