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BlueStar STING platform for analysis of protein structure / function relationship: designing agrochemicals to fit new protein targets for bacterial, fungal and insect control. Repositório Alice
NESHICH, G..
Blue Star STING suite of programs for comprehensive analysis of structure, function and stability of proteins and their complexes, has matured over a decade of development. We will present the in silico process for identification of the catalytic site amino acids by means of selecting a range for values for a set of the STING_DB parameters - protein structure descriptors.
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Bioinformática; Biologia molecular; Estrutura de proteínas; Processo in silico; Bioinformatics; Protein structure.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/949444
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Bone morphogenetic proteins: from structure to clinical use BJMBR
Granjeiro,J.M.; Oliveira,R.C.; Bustos-Valenzuela,J.C.; Sogayar,M.C.; Taga,R..
Bone morphogenetic proteins (BMPs) are multi-functional growth factors belonging to the transforming growth factor ß superfamily. Family members are expressed during limb development, endochondral ossification, early fracture, and cartilage repair. The activity of BMPs was first identified in the 1960s but the proteins responsible for bone induction were unknown until the purification and cloning of human BMPs in the 1980s. To date, about 15 BMP family members have been identified and characterized. The signal triggered by BMPs is transduced through serine/threonine kinase receptors, type I and II subtypes. Three type I receptors have been shown to bind BMP ligands, namely: type IA and IB BMP receptors and type IA activin receptors. BMPs seem to be...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bone morphogenetic proteins; Osteogenic protein; Protein structure; Meta-analysis; Clinical trial.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005001000003
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Building multiple sequence alignments with a flavor of HSSP alignments. Repositório Alice
HIGA, R. H.; CRUZ, S. A. B. da; KUSER, P. R.; YAMAGISHI, M. E. B.; FILETO, R.; OLIVEIRA, S. R. de M.; MAZONI, I.; SANTOS, E. H. dos; MANCINI, A. L.; NESHICH, G..
The present study describes the processing used for building SH2QS as well as a comparison of the degree of residue conservation reported by SH2QS and HSSP. The comparison of the profiles from two alignments is also presented.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Estrutura secundária de proteínas; Sting; Multiple sequence alignment; Residue conservation; Relative entropy; Bioinformatics; Protein structure; Protein secondary structure.
Ano: 2006 URL: http://www.alice.cnptia.embrapa.br/handle/doc/8262
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Characterization of a thermostable endoglucanase produced by Isoptericola variabilis sp. IDAH9 BJM
Azizi,Maryam; Hemmat,Jafar; Seifati,Seyed Morteza; Torktaz,Ibrahim; Karimi,Soodabeh.
Abstract This study aimed to isolate and evaluate the cellulase activity of cellulolytic bacteria in hot springs of Dehloran, Ilam province, Iran. Water and sludge samples were collected from the hot springs and the bacterial enrichment was performed in a medium containing rice barn and carboxymethyl cellulose (CMC). The cultures were incubated at 50 °C in aerobic conditions. The bacteria were isolated on CMC agar (1%) medium. Cellulase assay of the isolates was measured by the evaluation of endoglucanase enzyme activity, which is also called as carboxymethyl cellulase (CMCase). The isolated thermotolerant bacteria were then identified and optimized for the production of CMCase. Moreover, stabilizing elements of the enzyme were identified with in silico...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Carboxymethyl cellulase; Endoglucanase; Thermophiles; Protein structure.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822015000401225
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Cloning and initial characterization of cellulolytic enzymes selected in a metagenomic approach. Repositório Alice
FAHEEM, M.; VIDAL, J. F. D.; FERNANDES, J. P. C.; OLIVEIRA. G. M.; CAROLINE, C. F.; SOUTO, B. de M.; PARACHIN, N. S.; QUIRINO, B. F.; BARBOSA, J. A. R. G..
2013
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Biofuel; Metagenome; Cellulose degradation; Enzymatic activity; Protein structure.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/961702
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Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures. Repositório Alice
ROCCHIA, W.; NESHICH, G..
Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB)...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Biomoléculas; Banco de dados; Electrostatic potential of biomolecules; Protein structure analysis; Sting; Proteína; Bioinformatics; Protein structure.
Ano: 2007 URL: http://www.alice.cnptia.embrapa.br/handle/doc/899
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Predicting enzyme class from protein structure using Bayesian classification. Repositório Alice
BORRO, L. C.; OLIVEIRA, S. R. M.; YAMAGISHI, M. E. B.; MANCINI, A. L.; JARDINE, J. G.; MAZONI, I.; SANTOS, E. H. dos; HIGA, R. H.; KUSER, P. R.; NESHICH, G..
ABSTRACT. Predicting enzyme class from protein structure parameters is a challenging problem in protein analysis. We developed a method to predict enzyme class that combines the strengths of statistical and data-mining methods. This method has a strong mathematical foundation and is simple to implement, achieving an accuracy of 45%. A comparison with the methods found in the literature designed to predict enzyme class showed that our method outperforms the existing methods.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Estrutura de proteína; Classe de enzima; Bayesian classification; Protein function prediction; Naive Bayes; Enzyme classification number; Bayesian classifier; Data classification; Bioinformatics; Protein structure.
Ano: 2006 URL: http://www.alice.cnptia.embrapa.br/handle/doc/9196
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Prediction of binding hot spot residues by using structural and evolutionary parameters. Repositório Alice
HIGA, R. H.; TOZZI, C. L..
In this work, we present a method for predicting hot spot residues by using a set of structural and evolutionary parameters. Unlike previous studies, we use a set of parameters which do not depend on the structure of the protein in complex, so that the predictor can also be used when the interface region is unknown. Despite the fact that no information concerning proteins in complex is used for prediction, the application of the method to a compiled dataset described in the literature achieved a performance of 60.4%, as measured by F-Measure, corresponding to a recall of 78.1% and a precision of 49.5%. This result is higher than those reported by previous studies using the same data set.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Estrutura proteica; Interações proteína-proteína; Previsão de resíduos hot spots; Protein structure; Prediction.
Ano: 2009 URL: http://www.alice.cnptia.embrapa.br/handle/doc/875214
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Prediction of binding hot spot residues by using structural and evolutionary parameters Genet. Mol. Biol.
Higa,Roberto Hiroshi; Tozzi,Clésio Luis.
In this work, we present a method for predicting hot spot residues by using a set of structural and evolutionary parameters. Unlike previous studies, we use a set of parameters which do not depend on the structure of the protein in complex, so that the predictor can also be used when the interface region is unknown. Despite the fact that no information concerning proteins in complex is used for prediction, the application of the method to a compiled dataset described in the literature achieved a performance of 60.4%, as measured by F-Measure, corresponding to a recall of 78.1% and a precision of 49.5%. This result is higher than those reported by previous studies using the same data set.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Hot spots prediction; Protein structure; Hot spots.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300029
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T25: Multiple Structures - Selected Parameter (MSSP) 2D Plot. Repositório Alice
NESHICH, G..
The Multiple Structures - Single Parameter 2D module allows a user to compare, in a simple yet intuitive 2D plot, any one of the 150 different sequence, structure, function and stability parameters / descriptors, stored in STING_DB, for any protein structure deposited in the PDB. The 2D plot shows (for a selected parameter / descriptor) the numerical values in the Y-axis and the sequence residue numbers for structurally aligned proteins, in the X-axis. The MSSP module is a part of the improved Blue Star STING protein structure analysis computer interface and DB (which contains per-residue-reported descriptors (available for display both numerically and graphically) for either the public protein data base (the PDB)) or local files. The MSSP allows a user to...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Sting; Estrutura de proteínas; Protein structure.
Ano: 2010 URL: http://www.alice.cnptia.embrapa.br/handle/doc/876488
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The specificity of interactions between proteins and sulfated polysaccharides Anais da ABC (AABC)
Mulloy,Barbara.
Sulfated polysaccharides are capable of binding with proteins at several levels of specificity. As highly acidic macromolecules, they can bind non-specifically to any basic patch on a protein surface at low ionic strength, and such interactions are not likely to be physiologically significant. On the other hand, several systems have been identified in which very specific substructures of sulfated polysaccharides confer high affinity for particular proteins; the best-known example of this is the pentasaccharide in heparin with high affinity for antithrombin, but other examples may be taken from the study of marine invertebrates: the importance of the fine structure of dermatan sulfate (DS) to its interaction with heparin cofactor II (HCII), and the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Sulfated polysaccharides; Fucans; Dermatan sulfate; Heparan sulfate; Heparin; Protein structure; Growth factors; Development.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652005000400007
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The Star STING server: a multiplatform environment for protein structure analysis. Repositório Alice
NESHICH, G.; MAZONI, I.; OLIVEIRA, S. R. M.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R.; BORRO, L. C.; MORITA, D. U.; SOUZA, K. R. R.; ALMEIDA, G. V.; RODRIGUES, D. N.; JARDINE, J. G.; TOGAWA, R. C.; MANCINI, A. L.; HIGA, R. H.; CRUZ, S. A. B.; VIEIRA, F. D.; SANTOS, E. H.; MELO, R. C.; SANTORO, M. M..
ABSTRACT. Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Estrutura de proteina; Protein structure analysis; Sting; Per-residue structure descriptors; Topology similarity; Structure summaries; Bioinformatics; Protein structure.
Ano: 2006 URL: http://www.alice.cnptia.embrapa.br/handle/doc/9170
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The structural molecular biology network of the State of São Paulo, Brazil Anais da ABC (AABC)
Barbosa,João A.R.G.; Netto,Luis E.S.; Farah,Chuck S.; Schenkman,Sergio; Meneghini,Rogério.
This article describes the achievements of the Structural Molecular Biology Network (SMolBNet), a collaborative program of structural molecular biology, centered in the State of São Paulo, Brazil, and supported by São Paulo State Funding Agency (FAPESP). It gathers twenty scientific groups and is coordinated by the scientific staff of the Center of Structural Molecular Biology, at the National Laboratory of Synchrotron Light (LNLS), in Campinas. The SMolBNet program has been aimed at 1) solving the structure of proteins of interest related to the research projects of the groups. In some cases, the choice has been to select proteins of unknown function or of possible novel structure obtained from the sequenced genomes of the FAPESP genomic program; 2)...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Structural genomics; Protein crystallography; Nuclear magnetic resonance; Protein structure.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652006000200006
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Zika virus proteins at an atomic scale: how does structural biology help us to understand and develop vaccines and drugs against Zika virus infection? J. Venom. Anim. Toxins incl. Trop. Dis.
Valente,Ana Paula; Moraes,Adolfo Henrique.
Abstract In Brazil and in other tropical areas Zika virus infection was directly associated with clinical complications as microcephaly in newborn children whose mothers were infected during pregnancy and the Guillain-Barré syndrome in adults. Recently, research has been focused on developing new vaccines and drug candidates against Zika virus infection since none of those are available. In order to contribute to vaccine and drug development efforts, it becomes important the understanding of the molecular basis of the Zika virus recognition, infection and blockade. To this purpose, it is essential the structural determination of the Zika virus proteins. The genome sequencing of the Zika virus identified ten proteins, being three structural (protein E,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Zika virus proteins; Structural biology; Protein structure; Nuclear magnetic resonance spectroscopy; Protein-antibody interaction; Protein-small compound interaction.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992019000100206
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水稻白葉枯病抗性基因之蛋白質胺基酸的多變數分析 Taiwan Agricultural Research Institute
魏夢麗; 鍾依涵; 呂椿棠; 呂秀英; Meng-Li Wei; Yi-Han Chung; Chun-Tang Lu; Hsiu-Ying Lu.
[[abstract]]蛋白質中的胺基酸組成隱藏甚多訊息,但其組成特性會因不同物種或物種內不同基 因而異,故蛋白質的胺基酸組成分析成為生物資訊研究的重要課題之一。胺基酸組成特 性是由多個物種或基因 (觀測值) 與20 種胺基酸之頻率 (變數) 所構成的資料矩陣來決 定,這種多維資料形式所含之訊息,最適合利用多變數分析 (multivariate analysis) 之統 計技術來解析。為促進水稻白葉枯病抗病基因 (Xa) 蛋白質序列的結構研究,有必要針 對所有已完全定序的Xa 基因進行蛋白質之胺基酸組成分析。基此,本研究以NCBI 公 共資料庫內已知序列的Xa1、xa5、xa13、Xa13、Xa21、Xa26 及Xa27 等基因共17 條蛋 白質序列為供試材料,綜合運用集群分析 (cluster analysis) 及對應分析 (correspondence analysis),來檢測不同Xa 基因之蛋白質胺基酸組成的變異形式。結果顯示,根據胺基酸 組成比例,可將Xa 基因及其家族分成六群,各群基因之蛋白質序列中各有偏好的胺基 酸。Xa1、Xa21、Xa26 及Xa27 基因之蛋白質序列中皆以白胺酸 (leucine) 出現頻率最高; xa13、Xa13 及Xa27 的丙胺酸 (alanine) 出現較多但絲胺酸 (serine) 較少;xa13 及Xa13 也有較多的纈胺酸 (valine);xa5 出現麩胺酸 (glutamic acid) 和酥胺酸 (threonine) 的頻 率遠高於其他基因;所有Xa 基因皆含有高比例的疏水性胺基酸。本研究揭示出多變數 分析之統計技術,可有效檢測出Xa 基因間蛋白質之胺基酸組成的變異形式。
Palavras-chave: 水稻 Xa基因 蛋白質結構 胺基酸組成及屬性 集群分析 對應分析 Rice (Oryza sativa L.); Xa genes; Protein structure; Composition and attribution of amino acids; Cluster analysis; Correspondence analysis [[classification]]6.
Ano: 2008
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