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  • 1
    Electronic Resource
    Electronic Resource
    Free energy determination of polypeptide conformations generated by molecular dynamics (1984)
    s.l. : American Chemical Society
    Macromolecules 17 (1984), S. 2044-2050 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00140a029
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Internal β-Turn Hydration: Crystallographic Evidence and Molecular Dynamics Simulation (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 9625-9631 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100023a047
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Relationship between conformation and geometry as evidenced by molecular dynamics simulation of Cα,α-dialkylated glycines (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 239-244 
    Details
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 4
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of the docking of substrates to proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 174-182 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; docking ; computer simulation ; substrate docking ; immunoglobulin ; rational drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190303
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  • 5
    Electronic Resource
    Electronic Resource
    Free energy calculations in globular proteins: Methods to reduce errors (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1229-1240 
    Details
    ISSN: 0192-8651
    Keywords: free energy calculations ; molecular dynamics ; ribonuclease A ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The calculation of free energies by computer simulation represents one of the most promising areas in molecular modeling. While the computational methods developed so far give reliable results for liquids or solutions, they are not satisfactory for globular proteins. The reproducibility of the data is poor due to several sources of error. The most important are due to the magnitude of the molecule's phase space, to the long relaxation time of the system, and to the singularity occurring when creating or annihilating atoms. In a previous study Simonson and Brünger reported the free energy differences calculated for three successive mutations in the ribonuclease-S system and revealed several sources of error. These errors were reanalyzed and the performance of several methods studied in order to reduce them. Different approaches of mutating the Hamiltonian are compared using the method proposed by Resat and Mezei and a modification of the method proposed by Cross. Procedures are also proposed to reduce the effects of the long relaxation time of the molecule, to bias the simulation toward the experimental structure, and to reduce large free energy derivative fluctuations. All these methods give reliable results when the mutation is carried out in a peptide in solution. When the mutation is carried out in a globular protein, the sources of errors are reduced but not eliminated. Although the investigated procedures and methods increase the reliability of free energy calculation, further improvements will be required.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1229-1240, 1998
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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