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  • 1
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    Safeguarding the integrity of protein archive (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-30
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berman, Helen M -- Kleywegt, Gerard J -- Nakamura, Haruki -- Markley, John L -- Burley, Stephen K -- P41 LM005799/LM/NLM NIH HHS/ -- England -- Nature. 2010 Jan 28;463(7280):425. doi: 10.1038/463425c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110969" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Protein/*ethics/*standards ; Ethics, Research ; Reproducibility of Results ; Scientific Misconduct
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Experimental data for structure papers (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, T Alwyn -- Kleywegt, Gerard J -- New York, N.Y. -- Science. 2007 Jul 13;317(5835):194-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17626864" target="_blank"〉PubMed〈/a〉
    Keywords: *Crystallography, X-Ray ; *Databases, Protein ; Periodicals as Topic/standards ; *Protein Conformation ; Proteins/*chemistry ; Publishing/*standards
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    SIFTS: Structure Integration with Function, Taxonomy and Sequences resource (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts ) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
    Electronic Resource
    Electronic Resource
    Assignment strategies in homonuclear three-dimensional proton NMR spectra of proteins (1990)
    s.l. : American Chemical Society
    Biochemistry 29 (1990), S. 1829-1839 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00459a024
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  • 5
    Electronic Resource
    Electronic Resource
    Report of a workshop on the use of statistical validators in protein X-ray crystallography (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 228-234 
    Details
    ISSN: 1399-0047
    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/S0907444995010638
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  • 6
    Electronic Resource
    Electronic Resource
    Efficient Rebuilding of Protein Structures (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 829-832 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A computer program, called OOPS, is described which facilitates and speeds up the process of rebuilding a protein structure inside its electron density and reduces the chances of local errors persevering throughout the crystallographic protein structure determination process. The program uses a set of criteria to judge how reasonable each protein residue is and it generates macros for the macromolecular crystallographic model-building program O [Jones, Zou, Cowan & Kjeldgaard (1991). Acta Cryst. A47, 110–119] which, when executed, will take the crystallographer on a journey along all suspect residues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996001783
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  • 7
    Electronic Resource
    Electronic Resource
    xdlMAPMAN and xdlDATAMAN – Programs for Reformatting, Analysis and Manipulation of Biomacromolecular Electron-Density Maps and Reflection Data Sets (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 826-828 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two user-friendly computer programs are described for use in macromolecular X-ray crystallography, xdlMAP-MAN provides an interface for electron-density map exchange between some of the most commonly used phase refinement, structure refinement and model- building programs. In addition, it contains several options to analyse and abstract such maps. xdlDATA-MAN provides similar functionality for the analysis and manipulation of macromolecular reflection data sets. Both programs have a simple graphical user interface, and their source code has been put into the public domain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995014983
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  • 8
    Electronic Resource
    Electronic Resource
    Use of Non-crystallographic Symmetry in Protein Structure Refinement (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 842-857 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and `random noise'. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from this laboratory in which the presence (and employment) of non-crystallographic symmetry was crucial to the solution and refinement of the structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995016477
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  • 9
    Electronic Resource
    Electronic Resource
    Detection, delineation, measurement and display of cavities in macromolecular structures (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 178-185 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993011333
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  • 10
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray analysis of recombinant bovine cellular retinoic acid-binding protein (1994)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 370-374 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of bovine cellular retinoic acid-binding protein (CRABPI) have been grown from protein expressed in E. coli. Two different crystal forms were obtained. Crystals containing protein with the ligand all-trans retinoic acid belong to space group P41 or P43, a = b = 41.36, c = 202.71 Å and diffract to 2.5 Å. Crystals of CRABP with the synthetic retinoid analogue Am80 diffract to 1.9 Å with space group P21 and cell dimensions a = 37.03, b = 105.93, c = 40.31 Å, β = 110.28°. Considerations in the crystallization of proteins with light-sensitive ligands are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444994001204
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