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Additional file 1. Code Snippets regarding DrugTax.

Structural characterization of proteins and their complexes is a fundamental part in understanding any biological phenomena. Yet, the experimental determination of the three‐dimensional (3D) structure of proteins and their complexes remains a challenging undertaking. In order to complement the experimental approaches, computational methods have been developed based on a variety of algorithms and models to fill the gap between the amount of sequences and structures. In this article, we review the most common methodological approaches currently used in the field, highlighting the ab initio structure prediction methods and methods for the prediction and structural modeling of protein–protein interfaces (PPIs). We particularly focus on the use of evolutionary information to guide the modeling process.

Microbial degradation is the most important process to remove organic pollutants in Waste Water Treatment Plants. Regarding chiral compounds this process is normally enantioselective and needs the suitable analytical methodology to follow the removal of both enantiomers in an accurate way. Thus, this paper describes the development and validation of an enantioselective High Performance Liquid Chromatography with Fluorescence Detection (HPLC-FD) method for simultaneous analysis of fluoxetine (FLX) and norfluoxetine (NFLX) in wastewater effluents. Briefly, this method preconcentrated a small volume of wastewater samples (50 mL) on 500 mg Oasis MCX cartridges and used HPLC-FD with a vancomycin-based chiral stationary phase under reversed mode for analyses. The optimized mobile phase was EtOH/aqueous ammonium acetate buffer (92.5/7.5, v/v ) at pH 6.8. The effect of EtOH percentage, buffer concentration, pH, column oven temperature and flow rate on chromatographic parameters was systematically investigated. The developed method was validated within the wastewater effluent used in microcosms laboratory assays. Linearity ( R 2 > 0.99), selectivity and sensitivity were achieved in the range of 4.0–60 ng mL −1 for enantiomers of FLX and 2.0–30 ng mL −1 for enantiomers of NFLX. The limits of detection were between 0.8 and 2.0 ng mL −1 and the limits of quantification were between 2.0 and 4.0 ng mL −1 for both enantiomers of FLX and the enantiomers of its demethylated metabolite NFLX. The validated method was successfully applied and proved to be robust to follow the degradation of both enantiomers of FLX in wastewater samples, during 46 days.

Organic and metallic pollutants are ubiquitous in the environment. Many metals are reported to be toxic to microorganisms and to inhibit biodegradation. The effect of the metals iron, copper and silver on the metabolism of Labrys portucalensis F11 and on fluorobenzene (FB) biodegradation was examined. The results indicate that the addition of 1 mM of Fe(2+) to the culture medium has a positive effect on bacterial growth and has no impact in the biodegradation of 1 and 2 mM of FB. The presence of 1 mM of Cu(2+) was found to strongly inhibit the growth of F11 cultures and to reduce the biodegradation of 1 and 2 mM of FB to ca. 50 %, with 80 % of stoichiometrically expected fluoride released. In the experiments with resting cells, the FB degraded (from 2 mM supplied) was reduced ca. 20 % whereas the fluoride released was reduced to 45 % of that stoichiometrically expected. Ag(+) was the most potent inhibitor of FB degradation. In experiments with growing cells, the addition of 1 mM of Ag(+) to the culture medium containing 1 and 2 mM of FB resulted in no fluoride release, whereas FB degradation was only one third of that observed in control cultures. In the experiments with resting cells, the addition of Ag(+) resulted in 25 % reduction in substrate degradation and fluoride release was only 20 % of that stoichiometrically expected. The accumulation of catechol and 4-fluorocatechol in cultures supplemented with Cu(2+) or Ag(+) suggest inhibition of the key enzyme of FB metabolism-catechol 1,2-dioxygenase.