• Publications
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Investigation of de novo Totally Random Biosequences, Part II
We present an investigation on theoretically possible protein structures which have not been selected by evolution and are, therefore, not present on our Earth (‘Never Born Proteins’ (NBP)). InExpand
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LIBRA-WA: a web application for ligand binding site detection and protein function recognition
TLDR
A web application based on an improved LIBRA engine, featuring a novel scoring scheme consistently improving LIBRA's performance and a refined algorithm that can identify binding sites hosted at the interface between different subunits. Expand
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The human iron exporter ferroportin. Insight into the transport mechanism by molecular modeling
TLDR
Structural models of ferroportin in the three mechanistically relevant conformations (inward open, occluded, and outward open) have been obtained. Expand
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Structure/function relationships in ceruloplasmin.
Ceruloplasmin belongs to the family of multinuclear copper oxidases, which also includes ascorbate oxidase and laccase (Solomon et al., 1996). These proteins are trinuclear copper cluster enzymes, asExpand
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ASSIST: a fast versatile local structural comparison tool
TLDR
We develop a fast and exclusively structure-based tool for searching structural similarity, which allows to predict the catalytic function, if any, of proteins. Expand
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LIBRA: LIgand Binding site Recognition Application
TLDR
LIBRA is a structure-based ligand binding site recognition application based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. Expand
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Massive non-natural proteins structure prediction using grid technologies
TLDR
We use the Rosetta model to predict the three-dimensional structures of randomly chosen natural proteins and show that they are compact, ordered and water-soluble. Expand
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An Automatic Identification and Resolution System for Protein-Related Abbreviations in Scientific Papers
TLDR
We propose a methodology to identify and resolve proteinrelated abbreviations found in the full texts of scientific papers, as part of a semi-automatic process implemented in our PRAISED framework. Expand
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Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes,Expand
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The Production of de novo Folded Proteins by a Stepwise Chain Elongation: A Model for Prebiotic Chemical Evolution of Macromolecular Sequences
We describe an experimental procedure to mimic the formation of long (over 40 residues) co‐oligopetide sequences in many identical copies which may have occurred in the prebiotic molecular evolution.Expand
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