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  • 1995-1999  (3)
  • 1990-1994  (3)
  • Biochemistry  (3)
  • MCSS  (2)
  • disulfide bonds
  • 1
    Digitale Medien
    Digitale Medien
    An automated method for dynamic ligand design (1995)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 472-490 
    Details
    ISSN: 0887-3585
    Schlagwort(e): drug design ; FKBP ; FK506 ; immunophilin ; MCSS ; DLD ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site. © 1995 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/prot.340230403
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  • 2
    Digitale Medien
    Digitale Medien
    The contribution of cross-links to protein stability: A normal mode analysis of the configurational entropy of the native state (1993)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 15 (1993), S. 71-79 
    Details
    ISSN: 0887-3585
    Schlagwort(e): disulfide bonds ; protein stability ; entropy of proteins ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5-5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of crosslinks are discussed. © 1993 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/prot.340150109
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  • 3
    Digitale Medien
    Digitale Medien
    Functionality maps of binding sites: A multiple copy simultaneous search method (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 29-34 
    Details
    ISSN: 0887-3585
    Schlagwort(e): drug-design ; ligand-binding ; hemagglutinin ; functional groups ; MCSS ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A new method is proposed for determining energetically favorable positions and orientations for functional groups on the surface of proteins with known three-dimensional structure. From 1,000 to 5,000 copies of a functional group are randomly placed in the site and subjected to simultaneous energy minimization and/or quenched molecular dynamics. The resulting functionality maps of a protein receptor site, which can take account of its flexibility, can be used for the analysis of protein ligand interactions and rational drug design. Application of the method to the sialic acid binding site of the influenza coat protein, hemagglutinin, yields functional group minima that correspond with those of the ligand in a cocrystal structure.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/prot.340110104
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  • 4
    Digitale Medien
    Digitale Medien
    A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 700-733 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portions of the system; cases in which the QM and MM methodology is applied to parts of the same molecule or to different molecules are considered. The details of the method and a range of test calculations, including comparisons with ab initio and experimental results, are given. It is found that in many cases satisfactory results are obtained. However, there are limitations to this type of approach, some of which arise from the AM1 or MNDO methods themselves and others from the present QM/MM implementation. This suggests that it is important to test the applicability of the method to each particular case prior to its use. Possible areas of improvement in the methodology are discussed.
    Zusätzliches Material: 15 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540110605
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  • 5
    Digitale Medien
    Digitale Medien
    Harmonic analysis of large systems. I. Methodology (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1522-1542 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Methods have been developed for the determination of vibrational frequencies and normal modes of large systems in the full conformational space (including all degrees of freedom) and in a reduced conformational space (reducing the number of degrees of freedom). The computational method, which includes Hessian generation and storage, full and iterative diagonalization techniques, and the refinement of the results, is presented. A method is given for the quasiharmonic analysis and the reduced basis quasiharmonic analysis. The underlying principle is that from the atomic fluctuations, an effective harmonic force field can be determined relative to the dynamic average structure. Normal mode analysis tools can be used to characterize quasiharmonic modes of vibration. These correspond to conventional normal modes except that anharmonic effects are included. Numerous techniques for the analyses of vibrational frequencies and normal modes are described. Criteria for the analysis of the similarity of low-frequency normal modes is presented. The approach to determining the natural frequencies and normal modes of vibration described here is general and applicable to any large system. © 1995 John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540161209
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  • 6
    Digitale Medien
    Digitale Medien
    Potential energy function for cation-peptide interactions: An ab initio study (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 690-704 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A potential energy function is developed to represent the interaction of small monovalent cations, Li+, Na+, and K+, with the backbone of polypeptides. The results are based on ab initio calculations up to the 6-31G* level of the interactions of the ions with acetamide and N-methylacetamide. Basis set superposition errors are corrected with the counterpoise method. A systematic overestimate of the bond polarities is taken into account by an empirical scaling procedure that uses the ratio of the experimental to ab initio dipole moment. The calculated binding energies obtained with this procedure show consistent convergence with different basis sets and are in good agreement with experimental data on cation-water and cation-dimethylformamide systems. Investigations of the calculated ab initio potential energy surface indicate that the cation-peptide interaction is dominated by electrostatics and includes a nonnegligible contribution from polarization of the peptide group by the ion. The induced polarization results in a steeper-than-Coulombic interaction and cannot be described by fixed ion-peptide partial charges electrostatics. Atomic polarizabilities located on the atoms of the ligand molecule are introduced to account for the induced polarization in the empirical energy function. A ∼1/r4 attractive interaction appears in the potential function. The resulting radial and angular dependence of the potential energy surface is well reproduced. © 1995 by John Wiley & Sons, Inc.
    Zusätzliches Material: 15 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540160605
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