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Träfflista för sökning "WFRF:(Vreven Thom) "

Search: WFRF:(Vreven Thom)

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1.
  • Moretti, Rocco, et al. (author)
  • Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
  • 2013
  • In: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 81:11, s. 1980-1987
  • Journal article (peer-reviewed)abstract
    • Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies. Proteins 2013; 81:1980-1987.
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2.
  • Zheng, Guishan, et al. (author)
  • Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method
  • 2009
  • In: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 109:9, s. 1841-1854
  • Journal article (peer-reviewed)abstract
    • We present the theoretical and implementation details of the DFTB method with analytical gradients into the Gaussian package. SCF optimization performance with DIIS method is compared with modified Broyden method and Anderson methods, from which DIIS method is to be preferred. The number of geometry optimization steps can be significantly decreased with the Berny algorithm compared to the conjugated gradient method. From the comparison of geometry parameters as well as trends in the change of HOMO and LUMO energies, the results show clearly that DFTB can reproduce values obtained at the B3LYP/6-31G(d) level well. We also investigated the DFTB method as the low level quantum mechanical (QM) method in an ONIOM (QM:QM') description for all amino acid model system and found DFTB promising as a method to describe polarization and charge-transfer effects in large systems.
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