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  1. AU="Debnath Pal"
  2. AU="Kamali Kakhki, Reza"
  3. AU=Mortele Koenraad J
  4. AU="Skaarup, Søren H"
  5. AU="Lin, Li-Er"
  6. AU=Goulard Marie
  7. AU=Rosner Mitchell H
  8. AU="Murphy, Bríd"
  9. AU="Tsuneyoshi, Isao"
  10. AU="Tram, Le Thi Hong"
  11. AU="Veli-Pekka Jaakola"
  12. AU="Erduğan, Hüseyin"

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  1. Artikel ; Online: Clusters of hairpins induce intrinsic transcription termination in bacteria

    Swati Gupta / Debnath Pal

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 18

    Abstract: Abstract Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently ... ...

    Abstract Abstract Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Cytochrome bc1-aa3 Oxidase Supercomplex As Emerging and Potential Drug Target Against Tuberculosis.

    Sindhu, Thangaraj / Debnath, Pal

    Current molecular pharmacology

    2021  Band 15, Heft 2, Seite(n) 380–392

    Abstract: The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. ...

    Abstract The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3 and its potential inhibitors in detail.
    Mesh-Begriff(e) Drug Delivery Systems ; Electron Transport Complex III ; Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism ; Humans ; Mycobacterium tuberculosis/metabolism ; Oxidoreductases ; Oxygen ; Tuberculosis/drug therapy
    Chemische Substanzen Oxidoreductases (EC 1.-) ; Electron Transport Complex IV (EC 1.9.3.1) ; Electron Transport Complex III (EC 7.1.1.8) ; Oxygen (S88TT14065)
    Sprache Englisch
    Erscheinungsdatum 2021-10-01
    Erscheinungsland United Arab Emirates
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 1874-4702
    ISSN (online) 1874-4702
    DOI 10.2174/1874467214666210928152512
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Network-based identification of miRNAs and transcription factors and in silico drug screening targeting δ-secretase involved in Alzheimer's disease

    Saleem Iqbal / Md. Zubbair Malik / Debnath Pal

    Heliyon, Vol 7, Iss 12, Pp e08502- (2021)

    2021  

    Abstract: Background: System medicine approaches have played a pivotal role in identifying novel disease networks especially in miRNA research. It is no wonder that miRNAs are implicated in multiple clinical conditions, allowing us to establish the hubs and nodes ... ...

    Abstract Background: System medicine approaches have played a pivotal role in identifying novel disease networks especially in miRNA research. It is no wonder that miRNAs are implicated in multiple clinical conditions, allowing us to establish the hubs and nodes for network models of Alzheimer's Disease (AD). AD is an age-related, progressive, irreversible, and multifactorial neurodegenerative disorder characterized by cognitive and memory impairment and is the most common cause of dementia in older adults. Worldwide, around 50 million people have dementia, and there are nearly 10 million new cases every year. δ-secretase, also known as asparagine endopeptidase (AEP) or legumain (LGMN), is a lysosomal cysteine protease that cleaves peptide bonds C-terminally to asparagine residues in both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in AD. The patient's miRNA expression was found to be deregulated in the brain, extracellular fluid, blood plasma, and serum. Methods: Protein-Protein Interaction (PPI) networks of LGMN or δ-secretase were constructed using the Genemania database. Network Analyzer, a Cytoscape plugin, analyzed the network topological properties of LGMN. miRNAs related to Alzheimer's were extracted from the HMDD (Human microRNA Disease Database) and experimentally verified miRNA-gene interaction was obtained by searching miRWalk. Starbase v2.0 and miRanda were used for screening miRNA of LGMN genes. Moreover, to understand the regulatory mechanism in AD, we have screened major transcription factors of LGMN targeted genes using the Network Analyst 3.0, TRRUST (v2.0) server, and ENCODE. The Genotype-Tissue Expression (GTEx) and BEST tool were used to investigate the expression pattern of the LGMN gene. In parallel, we performed in-silico drug designing of the novel inhibitor scaffold of δ-secretase as powerful therapeutic targets by using the concept of scaffolds and frameworks. In this context, this study also aimed at identifying effective small molecule inhibitors ...
    Schlagwörter Alzheimer's disease ; miRNA ; Systems medicine ; δ-secretase ; Molecular Dynamic Simulations ; Biomarker ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2021-12-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
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  4. Artikel ; Online: Sustained AMPK Activation and Proline Metabolism Play Critical Roles in the Survival of Matrix-Deprived Transformed Cells

    Manipa Saha / Neha Deshpande / Abhinav Dubey / Debnath Pal / Hanudatta S. Atreya / Annapoorni Rangarajan

    Frontiers in Cell and Developmental Biology, Vol

    2021  Band 9

    Abstract: Attachment to the matrix is critical for the survival of adherent cells, whereas detachment triggers death by apoptosis. Therefore, solid tumors must acquire the ability to survive the stress of matrix-detachment to transit through circulation and seed ... ...

    Abstract Attachment to the matrix is critical for the survival of adherent cells, whereas detachment triggers death by apoptosis. Therefore, solid tumors must acquire the ability to survive the stress of matrix-detachment to transit through circulation and seed metastases. Although a central role for energy metabolism in cancer progression is well established, what distinguishes its role in the cellular state of the matrix-deprived form compared to the matrix-attached form is not fully understood yet. Using an in vitro transformation model dependent on simian virus 40 (SV40) small t (ST) antigen for cellular survival and proliferation in matrix-deprived conditions, we demonstrate that 5′-adenosine monophosphate-activated protein kinase (AMPK) activity is elevated and sustained under matrix-deprived conditions in ST-expressing fibroblasts. Additionally, these cells display elevated energy (ATP) levels under matrix-deprived conditions in contrast to cells lacking ST expression. The elevated ATP levels are coupled to increased levels of proline in ST-expressing cells, as revealed by metabolomics studies. The AMPK-dependent upregulation of proline oxidase, an enzyme of proline degradation, is a key link for elevated ATP levels. This functional link is further established by proline supplementation concomitant with AMPK activation in matrix-deprived cells lacking ST antigen, yielding ATP and enhancing survival. Thus, our data establishes a key role for AMPK-dependent regulation of proline metabolism in mediating energy homeostasis and promoting survival of matrix-deprived cells. These findings identify key markers that distinguish the metabolic states of matrix-detached and matrix-attached transformed cells and have implications in developing novel therapeutic strategies for specifically targeting matrix-detached metastasizing cancer cells.
    Schlagwörter AMP-activated protein kinase (AMPK) ; anoikis ; anoikis-resistance ; matrix-deprivation ; proline oxidase (POX) ; proline metabolism ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 570
    Sprache Englisch
    Erscheinungsdatum 2021-11-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Serum biomarkers identification by iTRAQ and verification by MRM

    Anjali Arora / Vikas Patil / Paramita Kundu / Paturu Kondaiah / A. S. Hegde / A. Arivazhagan / Vani Santosh / Debnath Pal / Kumaravel Somasundaram

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in Glioblastoma

    2019  Band 12

    Abstract: Abstract Despite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4- ... ...

    Abstract Abstract Despite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4-plex iTRAQ methodology, we identified 40 proteins with differential abundance in GBM sera. The high abundance of serum S100A8/S100A9 was verified by multiple reaction monitoring (MRM). ELISA and MRM-based quantitation showed a significant positive correlation. Further, an integrated investigation using stromal, tumor purity and cell type scores demonstrated an enrichment of myeloid cell lineage in the GBM tumor microenvironment. Transcript levels of S100A8/S100A9 were found to be independent poor prognostic indicators in GBM. Medium levels of pre-operative and three-month post-operative follow-up serum S100A8 levels predicted poor prognosis in GBM patients who lived beyond median survival. In vitro experiments showed that recombinant S100A8/S100A9 proteins promoted integrin signalling dependent glioma cell migration and invasion up to a threshold level of concentrations. Thus, we have discovered GBM serum marker by iTRAQ and verified by MRM. We also demonstrate interplay between tumor micro and macroenvironment and identified S100A8 as a potential marker with diagnostic and prognostic value in GBM.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2019-02-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Exo-selective intermolecular Diels–Alder reaction by PyrI4 and AbnU on non-natural substrates

    Rajnandani Kashyap / Naga Veera Yerra / Joachyutharayalu Oja / Sandeepchowdary Bala / Gal Reddy Potuganti / Jagadeshwar Reddy Thota / Manjula Alla / Debnath Pal / Anthony Addlagatta

    Communications Chemistry, Vol 4, Iss 1, Pp 1-

    2021  Band 9

    Abstract: Diels-Alderases remain rare in nature, particularly those catalysing intermolecular reactions. Here two natural Diels-Alderases are shown to catalyse exo-selective intermolecular Diels-Alder reactions on non-natural substrates. ...

    Abstract Diels-Alderases remain rare in nature, particularly those catalysing intermolecular reactions. Here two natural Diels-Alderases are shown to catalyse exo-selective intermolecular Diels-Alder reactions on non-natural substrates.
    Schlagwörter Chemistry ; QD1-999
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Numerical simulation of a glucose sensitive composite membrane closed-loop insulin delivery system

    Mukherjee, Shashi Bajaj / Debabrata Datta / Soumyendu Raha / Debnath Pal

    Bioprocess and biosystems engineering. 2017 Oct., v. 40, no. 10

    2017  

    Abstract: Closed-loop insulin delivery system works on pH modulation by gluconic acid production from glucose, which in turn allows regulation of insulin release across membrane. Typically, the concentration variation of gluconic acid can be numerically modeled by ...

    Abstract Closed-loop insulin delivery system works on pH modulation by gluconic acid production from glucose, which in turn allows regulation of insulin release across membrane. Typically, the concentration variation of gluconic acid can be numerically modeled by a set of non-linear, non-steady state reaction diffusion equations. Here, we report a simpler numerical approach to time and position dependent diffusivity of species using finite difference and differential quadrature (DQ) method. The results are comparable to that obtained by analytical method. The membrane thickness directly determines the concentrations of the glucose and oxygen in the system, and inversely to the gluconic acid. The advantage with the DQ method is that its parameter values need not be altered throughout the analysis to obtain the concentration profiles of the glucose, oxygen and gluconic acid. Our work would be useful for modeling diabetes and other systems governed by such non-linear and non-steady state reaction diffusion equations.
    Schlagwörter analytical methods ; asymmetric membranes ; diabetes ; diffusivity ; equations ; gluconic acid ; glucose ; insulin ; mathematical models ; oxygen ; pH
    Sprache Englisch
    Erscheinungsverlauf 2017-10
    Umfang p. 1453-1462.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ZDB-ID 1476357-6
    ISSN 1432-0797 ; 1615-7605 ; 1615-7591
    ISSN (online) 1432-0797 ; 1615-7605
    ISSN 1615-7591
    DOI 10.1007/s00449-017-1803-1
    Datenquelle NAL Katalog (AGRICOLA)

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  8. Artikel: Mass Spectrometry-Based Diagnosis of Hemoglobinopathies: A Potential Tool for the Screening of Genetic Disorder

    Das, Rajdeep / Amit Kumar Mandal / Boby Mathew / Cecil Ross / Debnath Pal / Gopa Mitra / Vijay Bhat

    Biochemical genetics. 2016 Dec., v. 54, no. 6

    2016  

    Abstract: Hemoglobinopathies are caused by point mutation in globin gene that results in structural variant of hemoglobin. While 7 % of world populations are carrier of hemoglobinopathies, the prevalence of the disease varies between 3 to 17 % across different ... ...

    Abstract Hemoglobinopathies are caused by point mutation in globin gene that results in structural variant of hemoglobin. While 7 % of world populations are carrier of hemoglobinopathies, the prevalence of the disease varies between 3 to 17 % across different population groups in India. In a diagnostic laboratory, alkaline gel electrophoresis and cation exchange-based HPLC (CE-HPLC) are most widely used techniques for characterization of hemoglobin variants. In the above methods, the differential surface charge of hemoglobin molecule in variants is exploited for their characterization. Sometime, co-migration of variants in gel electrophoresis and co-elution or elution with unknown retention time in automated CE-HPLC might lead to ambiguity in the analysis of hemoglobinopathies. Under such circumstances, it is necessary to use other analytical methods that provide unambiguous results. Mass spectrometry-based proteomics approach and DNA sequence analysis are examples of such alternative methods. In the present study, liquid chromatography coupled to mass spectrometry has been used for three commonly observed variants in India, e.g., HbE, HbQ India and HbD Punjab that appeared with inappropriate results in the conventional analysis. A customized hemoglobin variant database has been used in the mass spectrometry-based analysis of those three variants. Mass spectrometry-based proteomics approach was used to analyze above variant sample accurately.
    Schlagwörter databases ; DNA ; gel electrophoresis ; genes ; genetic disorders ; hemoglobin ; high performance liquid chromatography ; mass spectrometry ; nucleotide sequences ; point mutation ; proteomics ; screening ; sequence analysis ; India
    Sprache Englisch
    Erscheinungsverlauf 2016-12
    Umfang p. 816-825.
    Erscheinungsort Springer US
    Dokumenttyp Artikel
    ZDB-ID 2168-4
    ISSN 1573-4927 ; 0006-2928
    ISSN (online) 1573-4927
    ISSN 0006-2928
    DOI 10.1007/s10528-016-9758-5
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  9. Artikel: Mass spectrometry based characterization of Hb Beckman variant in a falsely elevated HbA1c sample

    Das, Rajdeep / Amit Kumar Mandal / Boby Mathew / Cecil Ross / Debnath Pal / Gopa Mitra / Monita Muralidharan / Vijay Bhat

    Analytical biochemistry. 2015 Nov. 15, v. 489

    2015  

    Abstract: Glycated hemoglobin (HbA1c) is a ‘gold standard’ biomarker for assessing the glycemic index of an individual. HbA1c is formed due to nonenzymatic glycosylation at N-terminal valine residue of the β-globin chain. Cation exchange based high performance ... ...

    Abstract Glycated hemoglobin (HbA1c) is a ‘gold standard’ biomarker for assessing the glycemic index of an individual. HbA1c is formed due to nonenzymatic glycosylation at N-terminal valine residue of the β-globin chain. Cation exchange based high performance liquid chromatography (CE–HPLC) is mostly used to quantify HbA1c in blood sample. A few genetic variants of hemoglobin and post-translationally modified variants of hemoglobin interfere with CE–HPLC-based quantification, resulting in its false positive estimation. Using mass spectrometry, we analyzed a blood sample with abnormally high HbA1c (52.1%) in the CE–HPLC method. The observed HbA1c did not corroborate the blood glucose level of the patient. A mass spectrometry based bottom up proteomics approach, intact globin chain mass analysis, and chemical modification of the proteolytic peptides identified the presence of Hb Beckman, a genetic variant of hemoglobin, in the experimental sample. A similar surface area to charge ratio between HbA1c and Hb Beckman might have resulted in the coelution of the variant with HbA1c in CE–HPLC. Therefore, in the screening of diabetes mellitus through the estimation of HbA1c, it is important to look for genetic variants of hemoglobin in samples that show abnormally high glycemic index, and HbA1c must be estimated using an alternative method.
    Schlagwörter biomarkers ; blood glucose ; blood sampling ; cation exchange ; diabetes mellitus ; genetic variation ; glycemic index ; glycohemoglobin ; glycosylation ; hemoglobin ; high performance liquid chromatography ; mass spectrometry ; patients ; peptides ; proteolysis ; proteomics ; screening ; surface area ; valine
    Sprache Englisch
    Erscheinungsverlauf 2015-1115
    Umfang p. 53-58.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 1110-1
    ISSN 1096-0309 ; 0003-2697
    ISSN (online) 1096-0309
    ISSN 0003-2697
    DOI 10.1016/j.ab.2015.07.010
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  10. Artikel: Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments

    Manikandan, Karuppasamy / Debnath Pal / Guna Seetharaman / Nathan E Brener / Sitharama S Iyengar / Suryanarayanarao Ramakumar

    Genome biology. 2008 Mar., v. 9, no. 3

    2008  

    Abstract: We have developed a geometric clustering algorithm using backbone φ,ψ angles to group conformationally similar peptide fragments of any length. By labeling each fragment in the cluster with the level-specific Gene Ontology 'molecular function' term of ... ...

    Abstract We have developed a geometric clustering algorithm using backbone φ,ψ angles to group conformationally similar peptide fragments of any length. By labeling each fragment in the cluster with the level-specific Gene Ontology 'molecular function' term of its protein, we are able to compute statistics for molecular function-propensity and p-value of individual fragments in the cluster. Clustering-cum-statistical analysis for peptide fragments 8 residues in length and with only trans peptide bonds shows that molecular function propensities ≥20 and p-values ≤0.05 can dissect fragments within a protein linked to the molecular function.
    Schlagwörter algorithms ; genes ; geometry ; proteins ; statistics
    Sprache Englisch
    Erscheinungsverlauf 2008-03
    Umfang p. 1914.
    Erscheinungsort Springer-Verlag
    Dokumenttyp Artikel
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2008-9-3-r52
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