A structure filter for the Eukaryotic Linear Motif Resource (2009)
Via, Allegra, Gould, Cathryn M, Gemünd, Christine, Gibson, Toby J, Helmer-Citterich, Manuela
Abstract Background Many proteins are highly modular, being assembled from globular domains and segments of natively disordered polypeptides. Linear motifs, short sequence modules functioning...
Structural motifs recurring in different folds recognize the same ligand fragments (2009)
Ausiello, Gabriele, Gherardini, Pier, Gatti, Elena, Incani, Ottaviano, Helmer-Citterich, Manuela
Abstract Background 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...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2008)
Bmc Bioinformatics, Manuela Helmer-citterich, Rita Casadio, Ro Guffanti, Giancarlo Mauri, Luciano Milanesi, ...
Ausiello, Gabriele, Gherardini, Pier Federico, Marcatili, Paolo, Tramontano, Anna, Via, Allegra, Helmer-Citterich, Manuela
Abstract Background 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...
Structure-based function prediction: approaches and applications (2008)
Gherardini, Pier Federico, Helmer-Citterich, Manuela
The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing...
Via, Allegra, Peluso, Daniele, Gherardini, Pier Federico, De Rinaldis, Emanuele, Colombo, Teresa, Ausiello, Gabriele, ...
3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching...
SH3-Hunter: discovery of SH3 domain interaction sites in proteins (2007)
Ferraro, Enrico, Peluso, Daniele, Via, Allegra, Ausiello, Gabriele, Helmer-Citterich, Manuela
SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more...
Ausiello, Gabriele, Peluso, Daniele, Via, Allegra, Helmer-Citterich, Manuela
Abstract Background 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...
Via, Allegra, Gherardini, Pier, Ferraro, Enrico, Ausiello, Gabriele, Scalia Tomba, Gianpaolo, Helmer-Citterich, Manuela
Abstract Background 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...
Bmc Bioinformatics, Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, ...
Research article False occurrences of functional motifs in protein sequences highlight evolutionary constraints
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites (2007)
Zanzoni, Andreas, Ausiello, Gabriele, Via, Allegra, Gherardini, Pier Federico, Helmer-Citterich, Manuela
Phosphorylation is the most common protein post-translational modification. Phosphorylated residues (serine, threonine and tyrosine) play critical roles in the regulation of many cellular processes....
Fabrizio Ferrè, Allegra Via, Gabriele Ausiello, Barbara Brannetti, Andreas Zanzoni, Manuela Helmer-Citterich
Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in...
iSPOT: A Web Tool for the Analysis and Recognition of Protein Domain Specificity (2006)
Barbara Brannetti, Andreas Zanzoni, Luisa Montecchi-Palazzi, Gianni Cesareni, Manuela Helmer-Citterich
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
Abstract The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005,...
A neural strategy for the inference of SH3 domain-peptide interaction specificity (2005)
Ferraro, Enrico, Via, Allegra, Ausiello, Gabriele, Helmer-Citterich, Manuela
Abstract Background 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...
Ausiello, Gabriele, Via, Allegra, Helmer-Citterich, Manuela
Abstract Background 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...
Ferrè, Fabrizio, Ausiello, Gabriele, Zanzoni, Andreas, Helmer-Citterich, Manuela
Abstract Background 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...
BMC Bioinformatics BioMed Central (2005)
Gabriele Ausiello, Allegra Via, Manuela Helmer-citterich
Research article Query3d: a new method for high-throughput analysis of functional residues in protein structures
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
pdbFun: mass selection and fast comparison of annotated PDB residues (2005)
Ausiello, Gabriele, Zanzoni, Andreas, Peluso, Daniele, Via, Allegra, Helmer-Citterich, Manuela
pdbFun (http://pdbfun.uniroma2.it) is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as...
Seq2Struct: a resource for establishing sequence-structure links (2005)
Via, Allegra, Zanzoni, Andreas, Helmer-Citterich, Manuela
Summary: Several methods for establishing cross-links between Protein Data Bank (PDB) structures or Structural Classification of Proteins (SCOP) domains and Swiss-Prot + TrEMBL sequences (or vice...
A structural study for the optimisation of functional motifs encoded in protein sequences (2004)
Via, Allegra, Helmer-Citterich, Manuela
Abstract Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or...
Seq2Struct: a resource for establishing sequence-structure links (2004)
Via, Allegra, Zanzoni, Andreas, Helmer-Citterich, Manuela
Summary: Several methods for establishing cross-links between PDB structures or SCOP domains and Swiss-Prot + TrEMBL sequences (or vice versa) rely on databases annotations. Alternatively, sequence...
SURFACE: a database of protein surface regions for functional annotation (2004)
Ferrè, Fabrizio, Ausiello, Gabriele, Zanzoni, Andreas, Helmer-Citterich, Manuela
The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions....
Seq2Struct: a resource for establishing sequence-structure links (2004)
Via, Allegra, Zanzoni, Andreas, Helmer-Citterich, Manuela
Summary: Several methods for establishing cross-links between PDB structures or SCOP domains and Swiss-Prot + TrEMBL sequences (or vice versa) rely on databases annotations. Alternatively, sequence...
Rune Linding, Christine Gemünd, Sophie Chabanis-davidson, Morten Mattingsdal, Scott Cameron, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
Fabrizio Ferrè, Allegra Via, Gabriele Ausiello, Barbara Brannetti, Andreas Zanzoni, Manuela Helmer-Citterich
Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in...
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
iSPOT: a web tool to infer the interaction specificity of families of protein modules (2003)
Brannetti, Barbara, Helmer-Citterich, Manuela
iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from...
iSPOT: A Web Tool for the Analysis and Recognition of Protein Domain Specificity (2001)
Barbara Brannetti, Andreas Zanzoni, Luisa Montecchi-Palazzi, Gianni Cesareni, Manuela Helmer-Citterich
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool...
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
iSPOT: a web tool to infer the interaction specificity of families of protein modules
Brannetti, Barbara, Helmer-Citterich, Manuela
iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from...
SURFACE: a database of protein surface regions for functional annotation
Ferrè, Fabrizio, Ausiello, Gabriele, Zanzoni, Andreas, Helmer-Citterich, Manuela
The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions....
pdbFun: mass selection and fast comparison of annotated PDB residues
Ausiello, Gabriele, Zanzoni, Andreas, Peluso, Daniele, Via, Allegra, Helmer-Citterich, Manuela
pdbFun () is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated...
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
iSPOT: a web tool to infer the interaction specificity of families of protein modules
Brannetti, Barbara, Helmer-Citterich, Manuela
iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from...
SURFACE: a database of protein surface regions for functional annotation
Ferrè, Fabrizio, Ausiello, Gabriele, Zanzoni, Andreas, Helmer-Citterich, Manuela
The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions....
pdbFun: mass selection and fast comparison of annotated PDB residues
Ausiello, Gabriele, Zanzoni, Andreas, Peluso, Daniele, Via, Allegra, Helmer-Citterich, Manuela
pdbFun () is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated...
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites
Zanzoni, Andreas, Ausiello, Gabriele, Via, Allegra, Gherardini, Pier Federico, Helmer-Citterich, Manuela
Phosphorylation is the most common protein post-translational modification. Phosphorylated residues (serine, threonine and tyrosine) play critical roles in the regulation of many cellular processes....
False occurrences of functional motifs in protein sequences highlight evolutionary constraints
Via, Allegra, Gherardini, Pier Federico, Ferraro, Enrico, Ausiello, Gabriele, Scalia Tomba, Gianpaolo, Helmer-Citterich, Manuela
A neural strategy for the inference of SH3 domain-peptide interaction specificity
Ferraro, Enrico, Via, Allegra, Ausiello, Gabriele, Helmer-Citterich, Manuela
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics
SH3-Hunter: discovery of SH3 domain interaction sites in proteins
Ferraro, Enrico, Peluso, Daniele, Via, Allegra, Ausiello, Gabriele, Helmer-Citterich, Manuela
SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more...
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
Via, Allegra, Peluso, Daniele, Gherardini, Pier Federico, De Rinaldis, Emanuele, Colombo, Teresa, Ausiello, Gabriele, ...
3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching...
Ausiello, Gabriele, Gherardini, Pier Federico, Marcatili, Paolo, Tramontano, Anna, Via, Allegra, Helmer-Citterich, Manuela
Ferrè, Fabrizio, Via, Allegra, Ausiello, Gabriele, Brannetti, Barbara, Zanzoni, Andreas, Helmer-Citterich, Manuela
Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in...
iSPOT: A Web Tool for the Analysis and Recognition of Protein Domain Specificity
Brannetti, Barbara, Zanzoni, Andreas, Montecchi-Palazzi, Luisa, Cesareni, Gianni, Helmer-Citterich, Manuela
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool...