P. Nuno Palma

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A new computationally efficient and automated "soft docking" algorithm is described to assist the prediction of the mode of binding between two proteins, using the three-dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works(More)
Parkinson's disease (PD) is a neurological disorder characterized by the degeneration of dopaminergic neurons, with consequent reduction in striatal dopamine levels leading to characteristic motor symptoms. The most effective treatment for this disease continues to be the dopamine replacement therapy with levodopa together with an inhibitor of aromatic(More)
An acid metal-contaminated soil from the Aljustrel mining area (a pyrite mine located in SW Portugal in the Iberian Pyrite Belt) was subjected to chemical characterisation and total metal quantification (Cd, Cr, Cu, Ni, Pb and Zn). Water-soluble metals were determined and a sequential extraction procedure was used to investigate metal speciation. Two(More)
The use of organic waste and compost as a source of organic matter and nutrients is a common practice to improve soil physico-chemical properties, meanwhile reducing the need for inorganic fertilisers. Official guidelines to assess sewage sludge and compost quality are mostly based on total metal content of these residues. Measurement of the total(More)
This article describes the method and results of our participation in the Critical Assessment of PRediction of Interactions (CAPRI) experiment, using the protein docking program BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) (Palma et al., Proteins 2000;39:372-384). Of five target complexes (CAPRI targets 2, 4, 5, 6, and 7), only(More)
BACKGROUND, AIM, AND SCOPE Freshwater reservoirs can be impacted by several hazardous substances through inputs from agricultural activity, sewage discharges, and groundwater leaching and runoff. The water quality assessment is very important for implementation of the monitoring and remediation programs to minimize the risk promoted by hazardous substances(More)
The purpose of this study was to evaluate the potential impact of the pesticides detected in the Alqueva reservoir (Guadiana Basin, South Iberian Peninsula) on the aquatic organisms belonging to this ecosystem. For this purpose, the occurrence and risk assessment of 25 pesticides and of a number of their degradation products were determined in the Alqueva(More)
The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that(More)
Ecotoxicological effects of the herbicide atrazine and the insecticides endosulfan sulphate and chlorpyrifos were evaluated using a test battery comprising aquatic organisms from different trophic levels. According to the categories established in the EU legislation, atrazine can be considered non-harmful for the species tested, while the insecticides can(More)
The three-dimensional X-ray structure of cytochrome c3 from a sulfate reducing bacterium, Desulfovibrio desulfuricans ATCC 27774 (107 residues, 4 heme groups), has been determined by the method of molecular replacement [Frazão et al. (1994) Acta Crystallogr. D50, 233-236] and refined at 1.75 A to an R-factor of 17.8%. When compared with the homologous(More)