Base de dados : MEDLINE
Pesquisa : E05.393.760.705 [Categoria DeCS]
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[PMID]:29442031
[Au] Autor:Peng Y; Xu B; Tang J; Wan Z; Sun H; Wang G; Zhu YS
[Ti] Título:Analysis of ABCG2 methylation in stool samples of Chinese healthy males by pyrosequencing.
[So] Source:Pharmazie;71(8):447-454, 2016 08 01.
[Is] ISSN:0031-7144
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:ABCG2, an efflux pump protein-BCRP coding gene, is involved in the acquisition of chemotherapeutic drug resistance. In recent years, the epigenetic regulation of ABCG2, such as DNA methylation, has become a research hotspot and been attracting widespread attention. Methylation Special PCR (MSP) has been the mainly used method for gene methylation detection for a long time. With the development of pyrosequencing (PSQ) instrument and the convenience, simpleness, and economical benefit it brings, it will become the mainstream method for gene methylation detection in the near future. This study aims to establish a pyrosequencing method for detecting the methylation sites on ABCG2 gene promoter up-stream region, the promoter region and the first exon region, and to detect the methylation level of each site in stool samples, respectively. Thus, it cannot only lay the methodological foundation for the study of BCRP-mediated multi-drug resistance mechanisms in tumor cells, but also can give knowledge of ABCG2 methylation distribution in the intestine of Chinese healthy males by detecting the ABCG2 methylation levels in stool samples as the exfoliated intestinal epithelial cells constantly shed into the stool.
[Mh] Termos MeSH primário: Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP/genética
Fezes/química
Proteínas de Neoplasias/genética
Análise de Sequência de Proteína/métodos
[Mh] Termos MeSH secundário: Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP/metabolismo
Adulto
Grupo com Ancestrais do Continente Asiático
Ilhas de CpG/genética
Metilação de DNA
Epigênese Genética
Éxons
Voluntários Saudáveis
Seres Humanos
Masculino
Proteínas de Neoplasias/metabolismo
Regiões Promotoras Genéticas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (ABCG2 protein, human); 0 (ATP Binding Cassette Transporter, Sub-Family G, Member 2); 0 (Neoplasm Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180215
[St] Status:MEDLINE
[do] DOI:10.1691/ph.2016.6559


  2 / 12453 MEDLINE  
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[PMID]:28453683
[Au] Autor:Necci M; Piovesan D; Dosztányi Z; Tosatto SCE
[Ad] Endereço:Department of Biomedical Sciences, University of Padua, 35121 Padova, Italy.
[Ti] Título:MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.
[So] Source:Bioinformatics;33(9):1402-1404, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases. Availability and Implementation: MobiDB-lite is available as part of the MobiDB database from URL: http://mobidb.bio.unipd.it/. An executable can be downloaded from URL: http://protein.bio.unipd.it/mobidblite/. Contact: silvio.tosatto@unipd.it. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Proteínas Intrinsicamente Desordenadas/metabolismo
Proteômica/métodos
Análise de Sequência de Proteína/métodos
Software
[Mh] Termos MeSH secundário: Consenso
Seres Humanos
Proteínas Intrinsicamente Desordenadas/química
Sensibilidade e Especificidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Intrinsically Disordered Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btx015


  3 / 12453 MEDLINE  
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[PMID]:29251806
[Au] Autor:Matthews B
[Ad] Endereço:Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
[Ti] Título:Tools for protein science.
[So] Source:Protein Sci;27(1):6-9, 2018 01.
[Is] ISSN:1469-896X
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Proteínas/química
[Mh] Termos MeSH secundário: Animais
Dicroísmo Circular
Microscopia Crioeletrônica
Cristalografia por Raios X
Seres Humanos
Ressonância Magnética Nuclear Biomolecular
Conformação Proteica
Análise de Sequência de Proteína
[Pt] Tipo de publicação:EDITORIAL; INTRODUCTORY JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171219
[St] Status:MEDLINE
[do] DOI:10.1002/pro.3351


  4 / 12453 MEDLINE  
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[PMID]:28454901
[Au] Autor:Wu S; Han J; Zhang X; Zhong D; Liu R
[Ad] Endereço:School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
[Ti] Título:A computational model for predicting integrase catalytic domain of retrovirus.
[So] Source:J Theor Biol;423:63-70, 2017 Jun 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Integrase catalytic domain (ICD) is an essential part in the retrovirus for integration reaction, which enables its newly synthesized DNA to be incorporated into the DNA of infected cells. Owing to the crucial role of ICD for the retroviral replication and the absence of an equivalent of integrase in host cells, it is comprehensible that ICD is a promising drug target for therapeutic intervention. However, annotated ICDs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. Accordingly, it is of great importance to put forward a computational ICD model in this work to annotate these domains in the retroviruses. The proposed model then discovered 11,660 new putative ICDs after scanning sequences without ICD annotations. Subsequently in order to provide much confidence in ICD prediction, it was tested under different cross-validation methods, compared with other database search tools, and verified on independent datasets. Furthermore, an evolutionary analysis performed on the annotated ICDs of retroviruses revealed a tight connection between ICD and retroviral classification. All the datasets involved in this paper and the application software tool of this model can be available for free download at https://sourceforge.net/projects/icdtool/files/?source=navbar.
[Mh] Termos MeSH primário: Domínio Catalítico
Biologia Computacional
Evolução Molecular
Integrases/química
Retroviridae/classificação
Análise de Sequência de Proteína
[Mh] Termos MeSH secundário: Simulação por Computador
Bases de Dados de Proteínas
Anotação de Sequência Molecular
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 2.7.7.- (Integrases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE


  5 / 12453 MEDLINE  
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[PMID]:29258861
[Au] Autor:Carcamo-Noriega EN; Olamendi-Portugal T; Restano-Cassulini R; Rowe A; Uribe-Romero SJ; Becerril B; Possani LD
[Ad] Endereço:Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Apartado Postal 510-3, Cuernavaca, Morelos 62210, Mexico. Electronic address: edsoncar@ibt.unam.mx.
[Ti] Título:Intraspecific variation of Centruroides sculpturatus scorpion venom from two regions of Arizona.
[So] Source:Arch Biochem Biophys;638:52-57, 2018 01 15.
[Is] ISSN:1096-0384
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:This study investigated geographic variability in the venom of Centruroides sculpturatus scorpions from different biotopes. Venom from scorpions collected from two different regions in Arizona; Santa Rita Foothills (SR) and Yarnell (Yar) were analyzed. We found differences between venoms, mainly in the two most abundant peptides; SR (CsEv2e and CsEv1f) and Yar (CsEv2 and CsEv1c) identified as natural variants of CsEv1 and CsEv2. Sequence analyses of these peptides revealed conservative amino acid changes between variants, which may underlie biological activity against arthropods. A third peptide (CsEv6) was highly abundant in the Yar venom compared to the SR venom. CsEv6 is a 67 amino acid peptide with 8 cysteines. CsEv6 did not exhibit toxicity to the three animal models tested. However, both venoms shared similarities in peptides that are predicted to deter predators. For example, both venoms expressed CsEI (lethal to chick) in similar abundance, while CsEd and CsEM1a (toxic to mammals) displayed only moderate variation in their abundance. Electrophysiological evaluation of CsEd and CsEM1a showed that both toxins act on the human sodium-channel subtype 1.6 (hNav 1.6). Complete sequencing revealed that both toxins are structurally similar to beta-toxins isolated from different Centruroides species that also target hNav 1.6.
[Mh] Termos MeSH primário: Proteínas de Artrópodes
Variação Genética
Venenos de Escorpião
Escorpiões
[Mh] Termos MeSH secundário: Animais
Arizona
Proteínas de Artrópodes/química
Proteínas de Artrópodes/genética
Proteínas de Artrópodes/toxicidade
Células CHO
Galinhas
Cricetulus
Gryllidae
Células HEK293
Seres Humanos
Camundongos
Canal de Sódio Disparado por Voltagem NAV1.6/genética
Canal de Sódio Disparado por Voltagem NAV1.6/metabolismo
Venenos de Escorpião/química
Venenos de Escorpião/genética
Venenos de Escorpião/toxicidade
Escorpiões/química
Escorpiões/genética
Análise de Sequência de Proteína
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Arthropod Proteins); 0 (Centruroides toxin); 0 (NAV1.6 Voltage-Gated Sodium Channel); 0 (SCN8A protein, human); 0 (Scorpion Venoms); 141322-33-0 (toxin 2, Centruroides noxius)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171221
[St] Status:MEDLINE


  6 / 12453 MEDLINE  
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[PMID]:28451973
[Au] Autor:Laskowski RA
[Ad] Endereço:European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. roman@ebi.ac.uk.
[Ti] Título:The ProFunc Function Prediction Server.
[So] Source:Methods Mol Biol;1611:75-95, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The ProFunc web server is a tool for helping identify the function of a given protein whose 3D coordinates have been experimentally determined or homology modeled. It uses a cocktail of both sequence- and structure-based methods to identify matches to other proteins that may, in turn, suggest the query protein's most likely function. The server was originally developed to aid the worldwide structural genomics effort at the start of the millennium. It accepts a file containing the protein's 3D coordinates in PDB format, and, when processing is complete, sends an email containing a link to the password-protected result pages. The results include an at-a-glance summary, as well as separate pages containing more detailed analyses. The server can be found at: http://www.ebi.ac.uk/thornton-srv/databases/profunc .
[Mh] Termos MeSH primário: Bases de Dados de Proteínas
Proteínas/análise
Proteínas/química
[Mh] Termos MeSH secundário: Biologia Computacional/métodos
Conformação Proteica
Análise de Sequência de Proteína
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_7


  7 / 12453 MEDLINE  
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[PMID]:28451972
[Au] Autor:Nielsen H
[Ad] Endereço:Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Bldg., 208, 3500 Kgs., Lyngby, Denmark. hnielsen@cbs.dtu.dk.
[Ti] Título:Predicting Secretory Proteins with SignalP.
[So] Source:Methods Mol Biol;1611:59-73, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:SignalP is the currently most widely used program for prediction of signal peptides from amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway, but are not necessarily secreted. After a brief introduction to the biology of signal peptides and the history of signal peptide prediction, this chapter will describe all the options of the current version of SignalP and the details of the output from the program. The chapter includes a case study where the scores of SignalP were used in a novel way to predict the functional effects of amino acid substitutions in signal peptides.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Sinais Direcionadores de Proteínas/fisiologia
Proteínas/química
Análise de Sequência de Proteína/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Proteínas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Protein Sorting Signals); 0 (Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_6


  8 / 12453 MEDLINE  
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[PMID]:28451967
[Au] Autor:Wei Q; McGraw J; Khan I; Kihara D
[Ad] Endereço:Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
[Ti] Título:Using PFP and ESG Protein Function Prediction Web Servers.
[So] Source:Methods Mol Biol;1611:1-14, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Elucidating biological function of proteins is a fundamental problem in molecular biology and bioinformatics. Conventionally, protein function is annotated based on homology using sequence similarity search tools such as BLAST and FASTA. These methods perform well when obvious homologs exist for a query sequence; however, they will not provide any functional information otherwise. As a result, the functions of many genes in newly sequenced genomes are left unknown, which await functional interpretation. Here, we introduce two webservers for function prediction methods, which effectively use distantly related sequences to improve function annotation coverage and accuracy: Protein Function Prediction (PFP) and Extended Similarity Group (ESG). These two methods have been tested extensively in various benchmark studies and ranked among the top in community-based assessments for computational function annotation, including Critical Assessment of Function Annotation (CAFA) in 2010-2011 (CAFA1) and 2013-2014 (CAFA2). Both servers are equipped with user-friendly visualizations of predicted GO terms, which provide intuitive illustrations of relationships of predicted GO terms. In addition to PFP and ESG, we also introduce NaviGO, a server for the interactive analysis of GO annotations of proteins. All the servers are available at http://kiharalab.org/software.php .
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Proteínas
Software
[Mh] Termos MeSH secundário: Algoritmos
Bases de Dados de Proteínas
Análise de Sequência de Proteína
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Proteins)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_1


  9 / 12453 MEDLINE  
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[PMID]:29293498
[Au] Autor:Menichelli C; Gascuel O; Bréhélin L
[Ad] Endereço:IBC, LIRMM, Univ. Montpellier, CNRS, Montpellier, France.
[Ti] Título:Improving pairwise comparison of protein sequences with domain co-occurrence.
[So] Source:PLoS Comput Biol;14(1):e1005889, 2018 01.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence.
[Mh] Termos MeSH primário: Proteínas/química
Proteínas/genética
Alinhamento de Sequência/métodos
Análise de Sequência de Proteína/métodos
[Mh] Termos MeSH secundário: Algoritmos
Sequência de Aminoácidos
Biologia Computacional
Bases de Dados de Proteínas
Plasmodium falciparum/química
Plasmodium falciparum/genética
Domínios Proteicos
Proteínas de Protozoários/química
Proteínas de Protozoários/genética
Alinhamento de Sequência/estatística & dados numéricos
Análise de Sequência de Proteína/estatística & dados numéricos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Proteins); 0 (Protozoan Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005889


  10 / 12453 MEDLINE  
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[PMID]:28460117
[Au] Autor:Huerta-Cepas J; Forslund K; Coelho LP; Szklarczyk D; Jensen LJ; von Mering C; Bork P
[Ad] Endereço:Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
[Ti] Título:Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.
[So] Source:Mol Biol Evol;34(8):2115-2122, 2017 Aug 01.
[Is] ISSN:1537-1719
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines are relatively inaccessible (e.g., new assignments only available through database updates), less precise homology-based functional transfer is still the default for (meta-)genome annotation. We, therefore, developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. To validate our method, we benchmarked Gene Ontology (GO) predictions against two widely used homology-based approaches: BLAST and InterProScan. Orthology filters applied to BLAST results reduced the rate of false positive assignments by 11%, and increased the ratio of experimentally validated terms recovered over all terms assigned per protein by 15%. Compared with InterProScan, eggNOG-mapper achieved similar proteome coverage and precision while predicting, on average, 41 more terms per protein and increasing the rate of experimentally validated terms recovered over total term assignments per protein by 35%. EggNOG-mapper predictions scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark. Finally, we evaluated eggNOG-mapper for functional annotation of metagenomics data, yielding better performance than interProScan. eggNOG-mapper runs ∼15× faster than BLAST and at least 2.5× faster than InterProScan. The tool is available standalone and as an online service at http://eggnog-mapper.embl.de.
[Mh] Termos MeSH primário: Alinhamento de Sequência/métodos
Análise de Sequência de Proteína/métodos
[Mh] Termos MeSH secundário: Algoritmos
Simulação por Computador
Bases de Dados Genéticas
Bases de Dados de Proteínas
Ontologia Genética
Genoma/genética
Filogenia
Alinhamento de Sequência/estatística & dados numéricos
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180201
[Lr] Data última revisão:
180201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/molbev/msx148



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