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  • 1
    Electronic Resource
    Electronic Resource
    Reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 14503-14511 
    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/bi00252a017
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    High-resolution proton nuclear magnetic resonance studies of human gastrin (1985)
    s.l. : American Chemical Society
    Biochemistry 24 (1985), S. 1720-1727 
    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/bi00328a023
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Local elevation: A method for improving the searching properties of molecular dynamics simulation (1994)
    Springer
    Journal of computer aided molecular design 8 (1994), S. 695-708 
    Details
    ISSN: 1573-4951
    Keywords: Conformational search ; Computer simulation ; Molecular dynamics ; Cyclosporin A
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124016
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation using weak-coupling NOE distance restraining (1996)
    Springer
    Journal of biomolecular NMR 8 (1996), S. 285-291 
    Details
    ISSN: 1573-5001
    Keywords: Time-averaged distance restraints ; Weak coupling ; MD simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Application of the weak-coupling scheme to restrain the configurations of a molecular system to a set of NOE distance restraints is investigated using two test systems: (i) a 15-atom chain molecule with one distance restraint; and (ii) a protein molecule with hundreds of NOE distance restraints. Atom-atom distance restraining by the weak-coupling technique is possible, but this method does not produce as good results as the penalty function method normally used to maintain NOE distance restraints.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00410327
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  • 5
    Electronic Resource
    Electronic Resource
    Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble (1995)
    Springer
    Journal of biomolecular NMR 6 (1995), S. 163-170 
    Details
    ISSN: 1573-5001
    Keywords: Ensemble averaging ; Time averaging ; Structure refinement ; Molecular dynamics ; Somatostatin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Time-averaging restraints in molecular dynamics simulations were introduced to account for the averaging implicit in spectroscopic data. Space- or molecule-averaging restraints have been used to overcome the fact that not all molecular conformations can be visited during the finite time of a simulation of a single molecule. In this work we address the issue of using the correct Boltzmann weighting for each member of an ensemble, both in time and in space. It is shown that the molecular- or space-averaging method is simple in theory, but requires a priori knowledge of the behaviour of a system. This is illustrated using a five-atom model system and the small cyclic peptide analogue somatostatin. When different molecular conformers that are separated by energy barriers insurmountable on the time scale of a simulation contribute significantly to a measured NOE intensity, the use of space- or molecule-averaged distance restraints yields a more appropriate description of the measured data than conventional single-molecule refinement with or without application of time averaging.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00211780
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  • 6
    Electronic Resource
    Electronic Resource
    Parametrisation of time-averaged distance restraints in MD simulations (1995)
    Springer
    Journal of biomolecular NMR 6 (1995), S. 313-320 
    Details
    ISSN: 1573-5001
    Keywords: Time-averaged distance restraints ; Parametrisation ; MD simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Time-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating or which grossly distort the dynamics of the system.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00197812
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  • 7
    Electronic Resource
    Electronic Resource
    Structure refinement using time-averaged J-coupling constant restraints (1993)
    Springer
    Journal of biomolecular NMR 3 (1993), S. 55-66 
    Details
    ISSN: 1573-5001
    Keywords: J-coupling ; Time averaging ; Structure refinement ; Computer simulation ; Molecular dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00242475
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  • 8
    Electronic Resource
    Electronic Resource
    Algorithms for clustering molecular dynamics configurations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1331-1340 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151203
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    Paper (German National Licenses)
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  • 9
    Electronic Resource
    Electronic Resource
    Protein structure prediction force fields: Parametrization with quasi-newtonian dynamics (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 367-384 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; force field ; structure prediction ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were-determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded-alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics. Proteins 27:367-384, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 10
    Electronic Resource
    Electronic Resource
    The dependence of amino acid pair correlations on structural environment (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 175-189 
    Details
    ISSN: 0887-3585
    Keywords: pairwise statistics ; secondary structure ; nonlocal interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A statistical analysis was performed to determine to what extent an amino acid determines the identity of its neighbors and to what extent this is determined by the structural environment. Log-linear analysis was used to discriminate chance occurrence from statistically meaningful correlations. The classification of structures was arbitrary, but was also tested for significance. A list of statistically significant interaction types was selected and then ranked according to apparent importance for applications such as protein design. This showed that, in general, nonlocal, through-space interactions were more important than those between residues near in the protein sequence. The highest ranked nonlocal interactions involved residues in β-sheet structures. Of the local interactions, those between residues i and i + 2 were the most important in both α-helices and β-strands. Some surprisingly strong correlations were discovered within β-sheets between residues and sites sequentially near to their bridging partners. The results have a clear bearing on protein engineering studies, but also have implications for the construction of knowledge-based force fields. Proteins 32:175-189, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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