Summary: Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of confidence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose J...

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to co...

SUMMARY Experimental MS(n) mass spectral libraries currently do not adequately cover chemical space. This limits the robust annotation of metabolites in metabolomics studies of complex biological samples. In silico fragmentation libraries would improve the identification of compounds from experimental multistage fragmentation data when experimental reference data are unavailable. Here, we prese...

A transaminase from Halomonas elongata and four mutants generated by an in silico-based design were recombinantly produced in E. coli, purified and applied to the amination of mono-substituted aromatic carbonyl-derivatives. While benzaldehyde derivatives were excellent substrates, only NO2-acetophenones were transformed into the (S)-amine with a high enantioselectivity. The different behaviour ...

We explore the advantages of DNA-like genomes for evolutionary computation in silico. Coupled with simulations of chemical reactions, these genomes offer greater efficiency, reliability, scalability, new computationally feasible fitness functions, and more dynamic evolutionary algorithms. The prototype application is the decision problem of HPP (the Hamiltonian Path Problem.) Other applications...

Associative memories based on DNA-affinity have been proposed [2]. Here, the performance, efficiency, reliability of DNA-based memories is quantified through simulations in silico. Retrievals occur reliably (98%) within very short times (milliseconds) despite the randomness of the reactions and regardless of the number of queries. The capacity of these memories is also explored in practice and ...

Synthetic biology, comprising many aspects including in vivo, in vitro and in silico techniques, models and methods, programming paradigms and tools, is a rapidly growing field with promising potential in building new synthetically constructed devices and systems. Synthetic biology features unconventional biological systems that do not naturally exist in nature. In this paper, we discuss a soft...

In silico metabolic reconstruction consists of deducing strain-specific metabolic pathways and other cellular characteristics only from the whole genome sequence. This task depends directly on: (i) the quality of the annotations to manage mining for enzymes in genomic data and (ii) the accurate description of metabolic pathways to be reconstructed. Here we present MetaboDB, a relational databas...

This paper describes the development of an in silico virtual screening application on Taiwan Unigrid. In silico virtual screening is one of the most promising approach to accelerate the drug development process. This pilot application implementation demonstrates the power of grid, which provides reliable service via shared computing resources. This development illustrates not only a new collabo...

The authors would like to thank PrioNet Canada for the opportunity to present these findings, the authors of the AGADIR method for providing their software, and NSERC Canada for their financial support. Acknowledgements and References Prion protein misfolding is responsible for the Transmissible Spongiform Encephalopathies (TSE) [1]. Experimental investigations suggest that the pathogen of prio...