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Sökning: WFRF:(Yusuf Dilmurat)

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2.
  • Grüning, Björn, et al. (författare)
  • Bioconda: A sustainable and comprehensive software distribution for the life sciences
  • 2017
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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3.
  • Marz, Manja, et al. (författare)
  • Animal snoRNAs and scaRNAs with exceptional structures
  • 2011
  • Ingår i: RNA Biology. - : Informa UK Limited. - 1547-6286 .- 1555-8584. ; 8:6, s. 938-946
  • Tidskriftsartikel (refereegranskat)abstract
    • The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A small group of diverse ncRNAs, however, shares the hallmarks of one or both classes of snoRNAs but differs substantially from the norm in some respects. Here, we compile the available information on these exceptional cases, conduct a thorough homology search throughout the available metazoan genomes, provide improved and expanded alignments, and investigate the evolutionary histories of these ncRNA families as well as their mutual relationships.
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4.
  • Yusuf, Dilmurat, et al. (författare)
  • An alternative method for the evaluation of docking performance : RSR vs RMSD.
  • 2008
  • Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 48:7, s. 1411-1422
  • Tidskriftsartikel (refereegranskat)abstract
    • A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 protein-ligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atoms-in our case the ligand-fits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed.
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  • Resultat 1-4 av 4

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