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  • 1
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    [Cham] : Springer
    Call number: 9783319325101 (e-book)
    Description / Table of Contents: This book will take an evidence-based approach to current knowledge about biomolecules and their place in our lives, inviting readers to explore how we know what we know, and how current gaps in knowledge may influence the way we approach the information. Biomolecular science is increasingly important in our everyday life, influencing the choices we make about our diet, our health, and our wellness. Often, however, information about biomolecular science is presented as a list of immutable facts, discouraging critical thought. The book will introduce the basic tools of structural biology, supply real-life examples, and encourage critical thought about aspects of biology that are still not fully understood.
    Type of Medium: 12
    Pages: 1 Online-Ressource (vii, 182 Seiten) , Illustrationen
    ISBN: 9783319325101 , 978-3-319-32510-1
    Language: English
    Note: Contents 1 The Protein Data Bank 2 Seeing Is Believing: Methods of Structure Solution 3 Visualizing the Invisible World of Molecules 4 The Twists and Turns of DNA 5 The Central Dogma 6 The Secret of Life: The Genetic Code 7 Evolution in Action 8 How Evolution Shapes Proteins 9 The Universe of Protein Folds 10 Order and Chaos in Protein Structure 11 Molecular Electronics 12 Green Energy 13 Peak Performance 14 Cellular Signaling Networks 15 GPCRs Revealed 16 Signaling with Hormones 17 Single-Molecule Chemistry: Enzyme Action and the Transition State 18 Seven Wonders of the World of Enzymes 19 Building Bodies 20 Coloring the Biological World 21 Amazing Antibodies 22 Attack and Defense: Weapons of the Immune System 23 Reconstructing HIV Erratum
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 16654-16661 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 1022-1029 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 4983-4993 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 105-153 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The majority of soluble and membrane-bound proteins in modern cells are symmetrical oligomeric complexes with two or more subunits. The evolutionary selection of symmetrical oligomeric complexes is driven by functional, genetic, and physicochemical needs. Large proteins are selected for specific morphological functions, such as formation of rings, containers, and filaments, and for cooperative functions, such as allosteric regulation and multivalent binding. Large proteins are also more stable against denaturation and have a reduced surface area exposed to solvent when compared with many individual, smaller proteins. Large proteins are constructed as oligomers for reasons of error control in synthesis, coding efficiency, and regulation of assembly. Symmetrical oligomers are favored because of stability and finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes. Asymmetry is also observed at several levels. Nearly all complexes show local asymmetry at the level of side chain conformation. Several complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation of dimers over complexes with higher cyclic symmetry, through a mechanism of prepositioned pairs of interacting residues. However, examples have been found for all of the crystallographic point groups, demonstrating that functional need can drive the evolution of any symmetry.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 11 (1997), S. 539-546 
    ISSN: 1573-4951
    Keywords: Rational drug design ; DNA-minor-groove-binding molecules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We report the design of optimal linker geometries for the synthesis of stapledDNA-minor-groove-binding molecules. Netropsin, distamycin, and lexitropsinsbind side-by-side to mixed-sequence DNA and offer an opportunity for thedesign of sequence-reading molecules. Stapled molecules, with two moleculescovalently linked side-by-side, provide entropic gains and restrain theposition of one molecule relative to its neighbor. Using a free-atom simulatedannealing technique combined with a discrete mutable atom definition, optimallengths and atomic composition for covalent linkages are determined, and anovel hydrogen bond ‘zipper’ is proposed to phase two molecules accuratelyside-by-side.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 10 (1996), S. 293-304 
    ISSN: 1573-4951
    Keywords: Inhibitor ; Receptor ; Simulated annealing ; Drug design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 0192-8651
    Keywords: automated docking ; binding affinity ; drug design ; genetic algorithm ; flexible small molecule protein interaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein-ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein-ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol-1 (2.177 kcal mol-1) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTODOCK, version 3.0.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1639-1662, 1998
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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