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Protocol
Motif Discovery from CLIP Experiments
RNA primary and secondary motif discovery is an important step in the annotation and characterization of unknown interaction dynamics between RNAs and RNA-Binding Proteins, and several methods have been develo...
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Article
Open AccessModeling cancer drug response through drug-specific informative genes
Recent advances in pharmacogenomics have generated a wealth of data of different types whose analysis have helped in the identification of signatures of different cellular sensitivity/resistance responses to h...
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Article
Open AccessAlternative splicing tends to avoid partial removals of protein-protein interaction sites
Anecdotal evidence of the involvement of alternative splicing (AS) in the regulation of protein-protein interactions has been reported by several studies. AS events have been shown to significantly occur in re...
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Article
Open AccessIdentification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities
The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation th...
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Article
Open AccessPhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae
Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the Leishmania genus undergo various developmental transitions in their life cycle triggered by changes in...
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Article
Open AccessStructural motifs recurring in different folds recognize the same ligand fragments
The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant pr...
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Article
Open AccessFunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate bind...
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Article
Open AccessLocal comparison of protein structures highlights cases of convergent evolution in analogous functional sites
We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only ...
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Article
Open AccessFalse occurrences of functional motifs in protein sequences highlight evolutionary constraints
False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a numerical approach to investigate the random a...
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Open AccessQuery3d: a new method for high-throughput analysis of functional residues in protein structures
The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known s...
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Article
Open AccessA neural strategy for the inference of SH3 domain-peptide interaction specificity
The SH3 domain family is one of the most representative and widely studied cases of so-called Peptide Recognition Modules (PRM). The polyproline II motif PxxP that generally characterizes its ligands does not ...
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Article
Open AccessFunctional annotation by identification of local surface similarities: a novel tool for structural genomics
Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in t...
