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  • 1
    Electronic Resource
    Electronic Resource
    Reconstruction of symmetry-related molecules from protein data bank (PDB) files (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 27 (1994), S. 1006-1009 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Many natural proteins are active as multimers. Crystallographic protein databases, however, generally store only part of the native multimer, the asymmetric unit, along with symmetry information. As a result of inaccuracies in the data, it is not always possible to reconstruct the native multimer. Here, a set of methods is presented that are designed to cope with inconsistencies in symmetry information. Applications include the validation of Protein Data Bank entries and the automatic generation of symmetry contacts for inspection and analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889894007764
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Structure of racemic 4-isopropenyl-1-cyclohexene-1-carbaldehyde oxime (perillartine) (1990)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 1133-1135 
    Details
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S010827019000107X
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  • 3
    Electronic Resource
    Electronic Resource
    Verification of Protein Structures: Side-Chain Planarity (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 29 (1996), S. 714-716 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Nine of the 20 natural amino acids contain a planar group in their side chains. For these groups, normal deviations from planarity were derived by the study of similar fragments in accurately determined small molecule structures. Comparison of these deviations with values found from a representative set of high-quality protein structures revealed that the planarity of the aromatic residues and arginine in protein structures is comparable to similar fragments in small molecules. For Asn, Gin, Asp and Glu, however, the deviations are up to twice as large as in comparable small-molecule structures, suggesting that adding an extra planarity restraint for these residue types could improve refinement procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889896008631
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  • 4
    Electronic Resource
    Electronic Resource
    3'-Methoxyspiro[bicyclo[3.1.0]hexane-6,16'-estra-1',3',5'(10')-trien]-17'-one (1995)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 721-723 
    Details
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108270194008899
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  • 5
    Electronic Resource
    Electronic Resource
    PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules (1996)
    Springer
    Journal of computer aided molecular design 10 (1996), S. 255-262 
    Details
    ISSN: 1573-4951
    Keywords: Molecular dynamics ; Graph theory ; SMILES
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A software package is described that operates on small molecules observed in the PDB collection of protein structures. Molecular topology files for many molecular modeling programs can be generated automatically. The three-dimensional coordinates of small molecules can be converted to molecular descriptor strings that encode them uniquely in order to enable small-molecule recognition, despite high variability in atom and molecule nomenclature. From this descriptor a plausible 3D structure can be regenerated using energy minimisation. Alternatively, an ensemble of structures can be generated using a distance-geometry-based algorithm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00355047
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  • 6
    Electronic Resource
    Electronic Resource
    The use of position-specific rotamers in model building by homology (1995)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 415-421 
    Details
    ISSN: 0887-3585
    Keywords: model building by homology ; position specific rotamers ; model evaluation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how to avoid the combinatorial explosion that results from the combination of many residues for which multiple good rotamers are predicted? We attempt to solve these problems by choosing position-specific rather than generalized rotamers and by sorting the residues that have to be modelled as a function of their freedom in rotamer space. The practical advantages of our method are the quality of the models for cases of high backbone similarity, the small amount of human intervention needed, and the fact that the method automatically estimates the reliability with which each residue has been modeled. Other methods described in this issue are probably more suitable if large backbone rearrangements or loop insertions and deletions need to be modeled. © 1995 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340230315
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