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  • 1
    Electronic Resource
    Electronic Resource
    Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins (1998)
    Springer
    Journal of molecular modeling 4 (1998), S. 347-354 
    Details
    ISSN: 0948-5023
    Keywords: Keywords Statistics ; Loop conformation ; Protein modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformations of protein loops from a non-redundant set of 347 proteins with less than 25% sequence homology have been studied in order to clarify the topological variation of protein loops. Loops have been classified in five types (α-α, α-β, β-α, β-links and β-hairpins) depending on the secondary structures that they embrace. Four variables have been used to describe the loop geometry (3 angles and the end-to-end distance between the secondary structures embracing the loop). Loops with well defined geometry are identified by means of the internal dependency between the geometrical variables by application of information-entropy theory. From this it has been deduced that loops formed by less than 10 residues show an intrinsic dependency on the geometric variables that defines the motif shape. In this interval the most stable loops are found for short connections owing to the entropic energy analysed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s008940050093
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  • 2
    Electronic Resource
    Electronic Resource
    Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2 (2000)
    Springer
    Journal of computer aided molecular design 14 (2000), S. 83-92 
    Details
    ISSN: 1573-4951
    Keywords: carboxypeptidases ; comparative modelling ; energy profiles ; molecular modelling ; secondary structure prediction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008197831529
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    Paper (German National Licenses)
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