Gabriele Ausiello

According to our database, Gabriele Ausiello authored at least 23 papers between 2003 and 2021.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2021

BRIO: a web server for RNA sequence and structure motif scan.

Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2021

2019

Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling.

Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini

PLoS Comput. Biol., 2019

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes.

Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich

Bioinform., 2019

2018

BEAM web server: a tool for structural RNA motif discovery.

Marco Pietrosanto, Marta Adinolfi, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich

Bioinform., 2018

2013

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

Luca Parca, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2013

webPDBinder: a server for the identification of ligand binding sites on protein structures.

Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello

Nucleic Acids Res., 2013

DBATE: database of alternative transcripts expression.

Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich

Database J. Biol. Databases Curation, 2013

2012

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello

BMC Bioinform., 2012

2011

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2011

2009

Structural motifs recurring in different folds recognize the same ligand fragments.

Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich

BMC Bioinform., 2009

2008

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2008

2007

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.

Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

SH3-Hunter: discovery of SH3 domain interaction sites in proteins.

Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

Nucleic Acids Res., 2007

False occurrences of functional motifs in protein sequences highlight evolutionary constraints.

Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich

BMC Bioinform., 2007

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.

Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2007

2006

A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity.

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

Bioinform., 2006

2005

pdbFun: mass selection and fast comparison of annotated PDB residues.

Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich

Nucleic Acids Res., 2005

Functional annotation by identification of local surface similarities: a novel tool for structural genomics.

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich

BMC Bioinform., 2005

A neural strategy for the inference of SH3 domain-peptide interaction specificity.

Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich

BMC Bioinform., 2005

Query3d: a new method for high-throughput analysis of functional residues in protein structures.

Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich

BMC Bioinform., 2005

2004

SURFACE: a database of protein surface regions for functional annotation.

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich

Nucleic Acids Res., 2004

2003

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.

Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson

Nucleic Acids Res., 2003