Learn More
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)
In this paper, we propose a constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA ("Dynamics algorithm for NMR applications " [1]) an existing commercial application based on simulated annealing. For(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)
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)
Bioinformatics is a rapidly growing field at the intersection of biology and computer science. As such, it poses a wealth of problems, opportunities and challenges for both areas. This paper overviews some of these issues, with an emphasis on those that seem most amenable to Constraint Programming (CP) approaches and where CP has made some progress. Since(More)
BACKGROUND The β-lactamase (bla) locus, which confers resistance to penicillins only, may control the transcription of mecA, the central element of methicillin resistance, which is embedded in a polymorphic heterelogous chromosomal cassette (the SCCmec element). In order to assess the eventual correlation between bla allotypes and genetic lineages, SCCmec(More)