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MOTIVATION Decomposing each protein into modular domains is a basic prerequisite to classify accurately structural units in biological molecules. Boundaries between domains are indicated by two similar amino acid sequence segments located within the same protein (repeats) or within homologous proteins at notably different distances from their respective N-(More)
MOTIVATION Genome sequencing projects require the periodic application of analysis tools that can classify and multiply align related protein sequence domains. Full automation of this task requires an efficient integration of similarity and alignment techniques. RESULTS We have developed a fully automated process that classifies entire protein sequence(More)
The KNOTTIN website and database organize information about knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology. Thanks to their small size and high stability, knottins provide appealing scaffolds for protein engineering and drug design. Static pages present the main historical and recent results about knottin(More)
The KNOTTIN database provides standardized information on the small disulfide-rich proteins with a knotted topology called knottins or inhibitor cystine knots. Static pages present the essential historical or recent results about knottin discoveries, sequences, structures, syntheses, folding, functions, applications and bibliography. New tools, KNOTER3D and(More)
PAT, for Protein Analysis Toolkit, is an integrated biocomputing server. The main goal of its design was to facilitate the combination of different processing tools for complex protein analyses and to simplify the automation of repetitive tasks. The PAT server provides a standardized web interface to a wide range of protein analysis tools. It is designed as(More)
BACKGROUND Present in various species, the knottins (also referred to as inhibitor cystine knots) constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic(More)
BACKGROUND Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold recognition. We propose a new automated method, EvDTree, based on a decision tree algorithm, for automatic derivation of amino acid substitution probabilities from a set of(More)
We propose in this paper a modular learning environment for protein modeling. In this system, the protein modeling problem is tackled in two successive phases. First, partial structural informations are determined via numerical learning techniques. Then, in the second phase, the multiple available informations are combined in pattern matching searches via(More)
Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. To get a deeper understanding of fungal effectors, we(More)
A generalization of the dynamic programming algorithm applied to the multiple alignment of protein sequences is proposed. The algorithm has two main procedures: (i) local correspondences between sequences-hereafter called anchor points-are selected according to a criterion that combines local and global simlilarity values, (ii) the alignment is constructed(More)