ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8048-8067 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two-dimensional adaptive umbrella sampling with the first umbrella coordinate equal to the potential energy of the system and the second umbrella coordinate equal to a function that discriminates important folded conformations from unfolded conformations is used to determine the equilibrium properties of complex biological systems. Compared to one-dimensional adaptive umbrella sampling with the potential energy as umbrella coordinate (multicanonical sampling), more reliable results can be obtained in certain cases. The method is applied to a helical peptide (RN24) with an analytical continuum solvent potential in combination with the PARAM19 force field of CHARMM. This effective potential energy function has been shown to describe the structural preferences of solvated peptides. With the two-dimensional approach and the deviation from the helical structure as the second umbrella coordinate, a converged description of the structural properties and the thermodynamics of the peptide RN24 is obtained. In particular, we find that the formation of the helix of RN24 occurs as a transition accompanied by a characteristic peak in the heat capacity. A formalism is described that uses the weighting factors obtained from a self-consistent solution of the weighted histogram analysis method equations to combine the results from a series of simulations with different biases and calculate the ensemble average of any dynamical variable as a function of the temperature without the need for extracting the density of states from the simulations. It is shown how the formalism can be used to calculate thermodynamic properties of the system. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480139
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 194-204 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Helical peptide ; β-Hairpin ; Random coil ; Umbrella sampling ; Multicanonical sampling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. To compare different implicit solvent potentials, the folding thermodynamics of the helical peptide RN24 and the β-hairpin peptide BH8 are studied by molecular dynamics simulation with adaptive umbrella sampling. As the potential energy functions, the analytical continuum solvent (ACS) potential and three simplified variants, termed EPSR1, EPSR4, and EPSR10, are used. The ACS potential is a combination of the standard CHARMM force field for the internal energy (bonds, angles, dihedrals) and the van der Waals energy with the analytical continuum electrostatic (ACE) potential and a non-polar solvation potential. The EPSR potentials differ from the ACS potential by the use of Coulomb's law with a distance-dependent dielectric function to calculate the electrostatic energy. With the ACS potential, quantitative agreement with experiment is obtained for the helix propensity (RN24: 62% calculated vs 50–60% experiment) and the β-hairpin propensity (BH8: 33% calculated vs 19–37% experiment) of the peptides. During the simulations with the EPSR potentials, no significant formation of secondary structure is observed. It is shown that the preference for coil conformations over conformations with secondary structure by the EPSR potentials is due to an overestimation of the energy of salt bridge formation, independent of the magnitude of the Coulomb energy relative to the other energy terms. Possible improvements of the distance-dependent dielectric functions which may permit their application to the simulation of peptide folding, are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050429
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    The program XEASY for computer-supported NMR spectral analysis of biological macromolecules (1995)
    Springer
    Journal of biomolecular NMR 6 (1995), S. 1-10 
    Details
    ISSN: 1573-5001
    Keywords: NMR structure determination ; Interactive computer graphics for support of NMR analysis ; Peak picking and integration ; Sequence-specific NMR assignments for biological macromolecules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of ‘strips’, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00417486
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Automated sequence-specific NMR assignment of homologous proteins using the program GARANT (1996)
    Springer
    Journal of biomolecular NMR 7 (1996), S. 207-213 
    Details
    ISSN: 1573-5001
    Keywords: NMR structure determination ; Automated sequence-specific resonance assignment ; Homologous proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The program GARANT (General Algorithm for Resonance AssignmeNT) for automated sequence-specific NMR assignment of proteins is based on the mapping of peaks predicted from the amino acid sequence onto the peaks observed in multidimensional spectra [C. Bartels, P. Güntert, M. Billeter and K. Wüthrich (1996) J. Comput. Chem., manuscript submitted for publication]. In this paper we demonstrate the potential of GARANT for the assignment of homologous proteins when either the three-dimensional structure or the chemical shifts of the parent protein are known. In these applications, GARANT utilizes supplementary information either in the form of interatomic distances derived from the three-dimensional structure, in order to add nuclear Overhauser effects reflecting the tertiary structure to the list of expected peaks, or in the form of the chemical shifts of the parent protein, in order to obtain a better estimate of the positions of the expected peaks. The procedure is illustrated with three different proteins: (i) a mutant form of Tendamistat (74 residues), using homonuclear 2D 1H NMR spectra and either the three-dimensional structure or the chemical shifts of the wild-type protein; (ii) the mutant Antp(C39S, W56S) homeodomain (68 residues), using homonuclear 2D 1H NMR spectra and the three-dimensional structure of the Antp(C39S) homeodomain; and (iii) free cyclophilin A (165 residues), using heteronuclear 3D NMR spectra and the three-dimensional structure of a cyclophilin A-cyclosporin A complex. In these three systems nearly complete assignment of the polypeptide backbone resonances and assignment of over 80% of the amino acid side-chain resonances was obtained without manual intervention.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00202037
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    A spectral correlation function for efficient sequential NMR assignments of uniformly 15N-labeled proteins (1994)
    Springer
    Journal of biomolecular NMR 4 (1994), S. 775-785 
    Details
    ISSN: 1573-5001
    Keywords: Proteins ; Sequential resonance assignment ; Interactive software XEASY
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A new computer-based approach is described for efficient sequence-specific assignment of uniformly 15N-labeled proteins. For this purpose three-dimensional 15N-correlated [1H, 1H]-NOESY spectra are divided up into two-dimensional 1H-1H strips which extend over the entire spectral width along one dimension and have a width of ca. 100 Hz, centered about the amide proton chemical shifts along the other dimension. A spectral correlation function enables sorting of these strips according to proximity of the corresponding residues in the amino acid sequence. Thereby, starting from a given strip in the spectrum, the probability of its corresponding to the C-terminal neighboring residue is calculated for all other strips from the similarity of their peak patterns with a pattern predicted for the sequentially adjoining residue, as manifested in the scalar product of the vectors representing the predicted and measured peak patterns. Tests with five different proteins containing both α-helices and β-sheets, and ranging in size from 58 to 165 amino acid residues show that the discrimination achieved between the sequentially neighboring residue and all other residues compares well with that obtained with an unguided interactive search of pairs of sequentially neighboring strips, with important savings in the time needed for complete analysis of 3D 15N-correlated [1H, 1H]-NOESY spectra. The integration of this routine into the program package XEASY ensures that remaining ambiguities can be resolved by visual inspection of the strips, combined with reference to the amino acid sequence and information on spin-system types obtained from additional NMR spectra.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00398408
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 62-66 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Adaptive umbrella sampling ; Multicanonical sampling ; Helical peptide ; β-hairpin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Adaptive umbrella sampling of the potential energy is used as a search method to determine the structures and thermodynamics of peptides in solution. It leads to uniform sampling of the potential energy, so as to combine sampling of low-energy conformations that dominate the properties of the system at room temperature with sampling of high-energy conformations that are important for transitions between different minima. A modification of the procedure for updating the umbrella potential is introduced to increase the number of transitions between folded and unfolded conformations. The method does not depend on assumptions about the geometry of the native state. Two peptides with 12 and 13 residues, respectively, are studied using the CHARMM polar-hydrogen energy function and the analytical continuum solvent potential for treatment of solvation. In the original adaptive umbrella sampling simulations of the two peptides, two and six transitions occur between folded and unfolded conformations, respectively, over a simulation time of 10 ns. The modification increases the number of transitions to 6 and 12, respectively, in the same simulation time. The precision of estimates of the average effective energy of the system as a function of temperature and of the contributions to the average effective energy of folded conformations obtained with the adaptive methods is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050407
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    RAPD analysis of genetic variation between a group of rose cultivars and selected wild rose species (1996)
    Springer
    Molecular breeding 2 (1996), S. 321-327 
    Details
    ISSN: 1572-9788
    Keywords: RAPD ; rose genetic variability ; molecular marker
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The genetic variability based on random-amplified polymorphic DNA markers was analysed among 10 cultivated rose varieties and 9 wild species from three different series of the genus Rosa. Using 13 different RAPD primers, 104 polymorphic DNA fragments with a high potential to differentiate rose genotypes could be produced. A dendrogram displaying the relative genetic similarities among the genotypes shows the existence of large genetic diversity among the cultivated roses as compared to the wild species. Furthermore, the main clusters found here are in agreement with known pedigrees and the classical taxonomy. However, the relationships between cultivated roses as inferred by RAPD markers do not correlate with the classical rose classification system. From the present data it is concluded that cultivated roses display a high level of genetic variability despite the fact that single morphological and physiological characters may be less polymorphic within rose groups. This contrasts with the widely accepted opinion of a lack of genetic variability in roses. This is also in accordance with the reported history of rose breeding which makes it highly probable that rose genomes comprise mosaics of different species genomes. As a consequence, it may be possible to utilize the high genetic variability of all genetic traits not under actual selection by breeders for future breeding programmes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00437910
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Fast algorithm for peptide sequencing by mass spectroscopy (1990)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 19 (1990), S. 363-368 
    Details
    ISSN: 1052-9306
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An automatic algorithm for sequencing polypeptides from fast atom bombardment tandem mass spectra is presented. Based on graph theory considerations it finds the most probable sequences, even if the amino acid composition is unknown, by scoring mass differences. The algorithm is fast as the computing time increases by less than the square of the number of amino acids. Pairs of two or three amino acids are proposed to explain the gap if peaks are missing.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bms.1200190607
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    GARANT-a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 139-149 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program for automatic resonance assignment of nuclear magnetic resonance (NMR) spectra of proteins, GARANT (General Algorithm for Resonance Assignment), is introduced. Three principal elements used in this approach are: (a) representation of resonance assignments as an optimal match of two graphs describing, respectively, peaks expected from combined knowledge of the primary structure and the magnetization transfer pathways in the spectra used, and experimentally observed peaks; (b) a scoring scheme able to distinguish between correct and incorrect resonance assignments; and (c) combination of an evolutionary algorithm with a local optimization routine. The score that evaluates the match of expected peaks to observed peaks relies on the agreement of the information available about these peaks, most prominently, but not exclusively, the chemical shifts. Tests show that the combination of an evolutionary algorithm and a local optimization routine yields results that are clearly superior to those obtained when using either of the two techniques separately in the search for the correct assignments. GARANT is laid out for assignment problems involving peaks observed in two- and three-dimensional homonuclear and heteronuclear NMR spectra of proteins. © 1997 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
  • 10
    Electronic Resource
    Electronic Resource
    Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1450-1462 
    Details
    ISSN: 0192-8651
    Keywords: adaptive umbrella sampling ; main chain ; side chain ; peptide conformations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new adaptive umbrella sampling technique for molecular dynamics simulations is described. The high efficiency of the technique renders multidimensional adaptive umbrella sampling possible and thereby enables uniform sampling of the conformational space spanned by several degrees of freedom. The efficiency is achieved by using the weighted histogram analysis method to combine the results from different simulations, by a suitable extrapolation scheme to define the umbrella potential for regions that have not been sampled, and by a criterion to identify simulations during which the system was not in equilibrium. The technique is applied to two test systems, the alanine dipeptide and the threonine dipeptide, to sample the configurational space spanned by one or two dihedral angles. The umbrella potentials applied at the end of each adaptive umbrella sampling run are equal to the negative of the corresponding potentials of mean force. The trajectories obtained in the simulations can be used to calculate dynamical variables that are of interest. An example is the distribution of the distance between the HN and the Hβ proton that can be important for the interpretation of NMR experiments. Factors influencing the accuracy of the calculated quantities are discussed.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1450-1462, 1997
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...