Kooperativer Bibliotheksverbund

Berlin Brandenburg

and
and

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Language
Year
  • 1
    Language: English
    In: Nucleic acids research, July 2014, Vol.42(Web Server issue), pp.W331-6
    Description: Unravelling the genotype-phenotype relationship in humans remains a challenging task in genomics studies. Recent advances in sequencing technologies mean there are now thousands of sequenced human genomes, revealing millions of single nucleotide variants (SNVs). For non-synonymous SNVs present in proteins the difficulties of the problem lie in first identifying those nsSNVs that result in a functional change in the protein among the many non-functional variants and in turn linking this functional change to phenotype. Here we present VarMod (Variant Modeller) a method that utilises both protein sequence and structural features to predict nsSNVs that alter protein function. VarMod develops recent observations that functional nsSNVs are enriched at protein-protein interfaces and protein-ligand binding sites and uses these characteristics to make predictions. In benchmarking on a set of nearly 3000 nsSNVs VarMod performance is comparable to an existing state of the art method. The VarMod web server provides extensive resources to investigate the sequence and structural features associated with the predictions including visualisation of protein models and complexes via an interactive JSmol molecular viewer. VarMod is available for use at http://www.wasslab.org/varmod.
    Keywords: Genetic Variation ; Models, Molecular ; Software ; Proteins -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    In: BJU International, July 2015, Vol.116(1), pp.109-116
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1111/bju.12894/abstract Byline: Kathie A. Wong, Rachael Mein, Mark Wass, Frances Flinter, Caroline Pardy, Matthew Bultitude, Kay Thomas Keywords: cystinuria; genetics; SLC3A1; SLC7A9; dibasic amino acids Objective To examine the genetic mutations in the first UK cohort of patients with cystinuria with preliminary genotype/phenotype correlation. Patients and Methods DNA sequencing and multiplex ligation-dependent probe amplification (MLPA) were used to identify the mutations in 74 patients in a specialist cystinuria clinic in the UK. Patients with type A cystinuria were classified into two groups: Group M patients had at least one missense mutation and Group N patients had two alleles of all other types of mutations including frameshift, splice site, nonsense, deletions and duplications. The levels of urinary dibasic amino acids, age at presentation of disease, number of stone episodes and interventions were compared between patients in the two groups using the Mann-Whitney U-test. Results In all, 41 patients had type A cystinuria, including one patient with a variant of unknown significance and 23 patients had type B cystinuria, including six patients with variants of unknown significance. One patient had three sequence variants in SLC7A9; however, two are of unknown significance. Three patients had type AB cystinuria. Three had a single mutation in SLC7A9. No identified mutations were found in three patients in either gene. There were a total of 88 mutations in SLC3A1 and 55 mutations in SLC7A9. There were 23 pathogenic mutations identified in our UK cohort of patients not previously published. In patients with type A cystinuria, the presence of a missense mutation correlated to lower levels of urinary lysine (mean [se] 611.9 [22.65] vs 752.3 [46.39] millimoles per mole of creatinine [mm/MC]; P=0.02), arginine (194.8 [24.83] vs 397.7 [15.32] mm/MC; P〈0.001) and ornithine (109.2 [7.40] vs 146.6 [12.7] mm/MC; P=0.02). There was no difference in the levels of urinary cystine (182.1 [8.89] vs 207.2 [19.23] mm/MC; P=0.23). Conclusions We have characterised the genetic diversity of cystinuria in a UK population including 23 pathogenic mutations not previously published. Patients with at least one missense mutation in SLC3A1 had significantly lower levels of lysine, arginine, and ornithine but not cystine than patients with all other combinations of mutations.
    Keywords: Cystinuria ; Genetics ; Slc 3a1 ; Slc 7a9 ; Dibasic Amino Acids
    ISSN: 1464-4096
    E-ISSN: 1464-410X
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Nucleic acids research, July 2010, Vol.38(Web Server issue), pp.W469-73
    Description: 3DLigandSite is a web server for the prediction of ligand-binding sites. It is based upon successful manual methods used in the eighth round of the Critical Assessment of techniques for protein Structure Prediction (CASP8). 3DLigandSite utilizes protein-structure prediction to provide structural models for proteins that have not been solved. Ligands bound to structures similar to the query are superimposed onto the model and used to predict the binding site. In benchmarking against the CASP8 targets 3DLigandSite obtains a Matthew's correlation co-efficient (MCC) of 0.64, and coverage and accuracy of 71 and 60%, respectively, similar results to our manual performance in CASP8. In further benchmarking using a large set of protein structures, 3DLigandSite obtains an MCC of 0.68. The web server enables users to submit either a query sequence or structure. Predictions are visually displayed via an interactive Jmol applet. 3DLigandSite is available for use at http://www.sbg.bio.ic.ac.uk/3dligandsite.
    Keywords: Software ; Structural Homology, Protein
    ISBN: 0002841489000
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    In: Journal of Emerging Diseases and Virology, 2016, Vol.2(3)
    ISSN: Journal of Emerging Diseases and Virology
    E-ISSN: 24731846
    Source: CrossRef
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    In: 2015, Vol.11(4), p.e1004150
    Description: The sequences that were chosen had recently been solved by X-ray crystallography but had not been not published or released until after the predictions from the community were made. Since the first CASP, we have seen many successful challenges, including Critical Assessment of Function Annotation (CAFA)...
    Keywords: Editorial
    ISSN: 1553-734X
    E-ISSN: 1553-7358
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: European Urology, March 2016, Vol.69(3), pp.543-544
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.eururo.2015.10.039 Byline: Kathie Alexina Wong, Mark Wass, Kay Thomas Author Affiliation: (a) Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London, SE1 9RT, UK (b) School of Biosciences, University of Kent, Canterbury Kent, UK Article History: Accepted 20 October 2015
    Keywords: Medicine
    ISSN: 0302-2838
    E-ISSN: 1873-7560
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Language: English
    In: Nucleic acids research, July 2012, Vol.40(Web Server issue), pp.W466-70
    Description: Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.
    Keywords: Software ; Proteins -- Physiology
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: Current Opinion in Structural Biology, 2011, Vol.21(3), pp.382-390
    Description: ► Conservation of interfaces and ligand binding site across structural space. ► Advances in methods for protein–protein interaction (PPI) prediction. ► Advances in methods for PPI interface prediction. ► Methods for the prediction of small molecule ligand binding sites. Macromolecular interactions are central to most cellular processes. Experimental methods generate diverse data on these interactions ranging from high throughput protein–protein interactions (PPIs) to the crystallised structures of complexes. Despite this, only a fraction of interactions have been identified and therefore predictive methods are essential to fill in the numerous gaps. Many predictive methods use information from related proteins. Accordingly, we review the conservation of interface and ligand binding sites within protein families and their association with conserved residues and Specificity Determining Positions. We then review recent developments in predictive methods for the identification of PPIs, protein interface sites and small molecule ligand binding sites. The challenges that are still faced by the community in these areas are discussed.
    Keywords: Biology ; Chemistry
    ISSN: 0959-440X
    E-ISSN: 1879-033X
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: Biochemical Society transactions, 15 August 2016, Vol.44(4), pp.973-8
    Description: The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in 〉28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches.
    Keywords: Ebola ; Pathogenicity ; Structural Bioinformatics ; Computational Biology -- Methods ; Disease Outbreaks -- Prevention & Control ; Ebolavirus -- Physiology ; Hemorrhagic Fever, Ebola -- Epidemiology
    ISSN: 03005127
    E-ISSN: 1470-8752
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    In: Bioinformatics, 2014, Vol. 30(14), pp.2091-2092
    Description: Contact: m.n.wass@kent.ac.uk or mark@wass.com
    Keywords: Biology;
    ISSN: 1367-4803
    E-ISSN: 1460-2059
    E-ISSN: 13674811
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages