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  • 1
    Electronic Resource
    Electronic Resource
    Gaussian-based Alignment of Protein Structures: Deriving a Consensus Superposition when Alternative Solutions Exist (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 539-549 
    Details
    ISSN: 0948-5023
    Keywords: Protein similarity ; Protein structure comparison ; Protein structure superposition ; Consensus alignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The use of a Gaussian-based representation of protein structures for evaluating protein-structure similarities and deriving three-dimensional superpositions is presented. The approach, as implemented in the program GAPS, is applied to three pairs of proteins with different topological characteristics (rich α-helix, mixed α-helix/β-strand, and rich β-strand), low sequence identities (10–30%), and recognized difficulties to define a unique optimum alignment.Validation of the GAPS superpositions is done by comparison with superpositions obtained by the TOP, GA_FIT, and ALIGN programs and those directly extracted from the FSSP database. Results suggest that a Gaussian-based methodology offers an objective means to, depending on the Gaussian-based representation, derive a consensus three-dimensional superposition when alternative superposition solutions exist.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060539
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching (2000)
    Springer
    Journal of computer aided molecular design 14 (2000), S. 39-51 
    Details
    ISSN: 1573-4951
    Keywords: flexible-conformations ; molecular alignments ; molecular-field similarity ; non-nucleoside HIV-1 reverse transcriptase inhibitors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract An analysis of the relationship among alignment solutions obtained from field-based matching of a representative set of rigid conformers of three non-nucleoside HIV-1 reverse transcriptase inhibitors and solutions obtained from flexible matching of the same conformers is presented. In some cases, different alignment solutions obtained from rigid matching converge to the same solution when conformational rigidity is relaxed, indicating that a reduced set of conformers per molecule may be sufficient in many field-based similarity studies. Furthermore, the results also indicate the importance of going beyond the pairwise similarity level to obtain consistent solutions in flexible-matching studies. In this respect, the best conformationally flexible multi-molecule alignment obtained is found to be in good agreement with the relative binding geometry and orientation found experimentally from protein-ligand crystal structures. The rms separation between corresponding atoms in computed and `experimental' sets of three inhibitor structures is 0.94 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008168228728
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Similarity versus docking in 3D virtual screening (2000)
    Springer
    Perspectives in drug discovery and design 20 (2000), S. 191-207 
    Details
    ISSN: 1573-9023
    Keywords: flexible ligand docking ; flexible ligand superposition ; molecular similarity ; thrombin ; virtual screening
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The development of similarity methods for fast flexible ligand superposition has recently received considerable attention. These efforts have brought similarity methods to a level of performance comparable to the well established protein-ligand docking methods for binding mode assessment and molecular database screening. However, the strengths and intrinsic limitations of both methodologies have been also stressed out extensively. As the number of resolved ligand-bound protein structures increases, combining ligand-based and receptor-based approaches emerges as a consensus strategy to maximally exploit the structural information available and improve the results obtained with either of the methods alone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008789224614
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    Paper (German National Licenses)
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