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- Jonsson, Anna-Li, et al.
(författare)
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Hanöbukten 2015
- 2016
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Ingår i: Faktablad: resultat från övervakningen av kustfisk.
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Annan publikation (populärvet., debatt m.m.)
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- Museth, Anna Katrine, et al.
(författare)
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Selective destabilization of the metal binding region caused by the FALS associated mutation G93A in CuZnSOD
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We have, by use of 1H-15N-HSQC NMR spectroscopy, analyzed hydrogen exchange at the amide groups of wtCuZnSOD and the FALS-associated G93A SOD-variant in their fully metallated states. From measurements at near physiological conditions we could analyze the exchange at 64% of all backbone amide groups, which have allowed a detailed characterization of the local dynamics at these positions in both the wt and G93A proteins. The results show that the G93A mutation had no effect on the dynamics at a majority of the investigated positions. However the mutation results in local destabilization at the site of mutation and to stabilization at positions that were apparently scattered over the entire protein surface. Most remarkably, the mutation selectively destabilized the remote metal binding region. The results indicate that the metal binding region may be involved in intermolecular protein-protein interactions, which may constitute the early stages in formation of aggregates.
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- Andersson, David C., 1978-, et al.
(författare)
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Design of target-tailored virtual screening experiments
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Discovering molecules with a desired biological function is one of the great challenges in drug research. To discover new lead molecules, in silico virtual screens (VS) are often conducted, in which databases of molecules are screened for potential binders to a specific protein, using molecular docking. The choice of docking software and parameter settings within the software can significantly influence the outcome of a VS. In this study, we have applied chemometric methods such as DoE, principal component analysis (PCA) and partial least-square projections to latent structure (PLS) to simulated VS experiments to find and compare suitable conditions for performing VS against six protein targets selected from the DUD databases. The docking parameters in FRED, and scoring functions in both FRED and GOLD docking software, were varied according to a statistical experimental design and a PLS model was calculated to correlate the experimental setup to the VS outcome. The study revealed that the choice of scoring function has the greatest influence on VS outcome, and that other parameters have varying influence, depending on the protein target. We also found that substantial bias can be introduced by the lack of variation of molecule properties in the databases used in the screening. The results indicate that docking experiments should be tailored to the protein target in order to obtain satisfactory VS results and that our methodology provides a suitable approach for such tailoring.
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- Björklund, Johanna, 1961-, et al.
(författare)
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A Comparative Evaluation of the Efficiency of N-Best Algorithms on Language Data
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The N-best extraction problem consists in selecting the N highest ranking hypotheses from a set of hypotheses, with respect to a given ranking system. In our setting, the hypotheses and ranking are jointly represented by a weighted tree automaton (wta) over the tropical semiring: the hypotheses are trees, or runs on trees, and the ranking is decided by the weight assigned to them. In previous work, we presented an algorithm for N-best extraction that combines techniques to restrict the search space, and proved it to be correct and efficient. The algorithm is now implemented in the software Betty, allowing us to complement the deductive study with an empirical investigation. In particular, we compare our algorithm to the state-of-the-art algorithm for extracting the N best runs, implemented in in the software toolkit Tiburon. The data sets used in the experiments are wtas resulting from real-world natural language processing tasks, as well as artificially created wtas with varying degrees of nondeterminism. We find that Betty outperforms Tiburon on all tested data sets.
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- Björklund, Johanna, 1961-, et al.
(författare)
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Faster Computation of N-Best Lists for Weighted Tree Automata
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We show that a previously proposed algorithm for the N-best trees problem – not to be confused with the easier N-best runs problem – can be made more efficient by changing how it arranges and explores the search space. Given an integer N and a weighted tree automaton (wta) M over the tropical semiring, the algorithm computes N trees of minimal weight with respect to M. Compared to the original algorithm, the modifications increase the laziness of the evaluation strategy, which makes the new algorithm asymptotically more efficient than its predecessor.
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