Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications (2009)
Fariselli, Piero, Savojardo, Castrense, Martelli, Pier, Casadio, Rita
Abstract Background Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative...
Sequence-based feature prediction and annotation of proteins (2009)
Juncker, Agnieszka S, Jensen, Lars J, Pierleoni, Andrea, Bernsel, Andreas, Tress, Michael L, Bork, Peer, ...
Abstract A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature...
On the Reconstruction of Three-dimensional Protein Structures from Contact Maps (2009)
Pietro Di Lena, Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
The problem of protein structure prediction is one of the long-standing goals of Computational Biology. Although we are still not able to provide first principle solutions, several shortcuts have...
Progress and challenges in predicting protein-protein interaction sites (2009)
Ezkurdia, Iakes, Bartoli, Lisa, Fariselli, Piero, Casadio, Rita, Valencia, Alfonso, Tress, Michael L.
The identification of protein–protein interaction sites is an essential intermediate step for mutant design and the prediction of protein networks. In recent years a significant number of methods...
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information (2009)
Bartoli, Lisa, Fariselli, Piero, Krogh, Anders, Casadio, Rita
Motivation:The widespread coiled-coil structural motif in proteins is known to mediate a variety of biological interactions. Recognizing a coiled-coil containing sequence and locating its coiled-coil...
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, ...
PredGPI: a GPI-anchor predictor (2008)
Pierleoni, Andrea, Martelli, Pier, Casadio, Rita
Abstract Background Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which is linked to the C-terminal...
Pier Luigi Martelli, Piero Fariselli, Luca Malaguti, Rita Casadio
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
is a professor of Biophysics at (2008)
Rita Casadio, Pier Luigi, Pier Luigi
and works on computational biology.
BIOINFORMATICS BaCelLo: a balanced subcellular localization predictor (2008)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Motivation. The knowledge of the subcellular localization of a protein is fundamental for elucidating its function. It is difficult to determine the subcellular location for eukaryotic cells with...
A three-state prediction of single point mutations on protein stability changes (2008)
Capriotti, Emidio, Fariselli, Piero, Rossi, Ivan, Casadio, Rita
Abstract Background A basic question of protein structural studies is to which extent mutations affect the stability. This question may be addressed starting from sequence and/or from structure. In...
Casadio, Rita, Martelli, Pier Luigi, Pierleoni, Andrea
Automated sequence annotation is a major goal of post-genomic era with hundreds of genomes in the databases, from both prokaryotes and eukaryotes. While the number of fully sequenced chromosomes from...
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps (2008)
Vassura, Marco, Margara, Luciano, Di Lena, Pietro, Medri, Filippo, Fariselli, Piero, Casadio, Rita
Summary: Fault Tolerant Contact Map Reconstruction (FT-COMAR) is a heuristic algorithm for the reconstruction of the protein three-dimensional structure from (possibly) incomplete (i.e. containing...
Predicting protein thermostability changes from sequence upon multiple mutations (2008)
Montanucci, Ludovica, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita
Motivation: A basic question in protein science is to which extent mutations affect protein thermostability. This knowledge would be particularly relevant for engineering thermostable enzymes. In...
Bmc Bioinformatics, Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio, Rita Casadio
A three-state prediction of single point mutations on protein stability changes
A back propagation neural network is trained on a non redundant data base comprising 200 chains to associate protein single sequences to their corresponding contact maps as evaluated from the protein...
Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli
A data base of minimally frustrated alpha helical segments is defined by filtering a set comprising 822 non redundant proteins, which contain 4783 alpha helical structures. The data base definition...
In silico evidence of the relationship between miRNAs and siRNAs (2007)
Montanucci, Ludovica, Fariselli, Piero, Martelli, Pier Luigi, Rossi, Ivan, Casadio, Rita
Both short interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate the repression of specific sequences of mRNA through the RNA interference pathway. In the last years several experiments have...
A three-state prediction of single point mutations on protein stability changes (2007)
Capriotti, Emidio, Fariselli, Piero, Rossi, Ivan, Casadio, Rita
A basic question of protein structural studies is to which extent mutations affect the stability. This question may be addressed starting from sequence and/or from structure. In proteomics and...
The WWWH of remote homolog detection: The state of the art (2007)
Fariselli, Piero, Rossi, Ivan, Capriotti, Emidio, Casadio, Rita
The detection of remote homolog pairs of proteins using computational methods is a pivotal problem in structural bioinformatics, aiming to compute protein folds on the basis of information in the...
Bartoli, Lisa, Calabrese, Remo, Fariselli, Piero, Mita, Damiano G, Casadio, Rita
Abstract Background Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2–5% of the genes encode for peptidases, irrespectively of...
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps (2007)
Luciano Margara, Marco Vassura, Pietro Lena, Piero Fariselli, Rita Casadio
PDF and gzipped PostScript formats via anonymous FTP from the areaftp.cs.unibo.it:/pub/TR/UBLCS or via WWW at
The implications of alternative splicing in the ENCODE protein complement (2007)
Tress, Michael L., Martelli, Pier L., Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan J., Yeats, Corin, ...
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological...
eSLDB: eukaryotic subcellular localization database (2007)
Pierleoni, Andea, Martelli, Pier Luigi, Fariselli, Piero, Casadio, Rita
Eukaryotic Subcellular Localization DataBase collects the annotations of subcellular localization of eukaryotic proteomes. So far five proteomes have been processed and stored: Homo sapiens, Mus...
Capriotti, Emidio, Casadio, Rita
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and...
The 4th Bologna Winter School: Hot Topics in Structural Genomics (2006)
The 4th Bologna Winter School on Biotechnologies was held on 9–15 February 2003 at the University of Bologna, Italy, with the specific aim of discussing recent developments in...
The Prediction of Membrane Protein Structure and Genome Structural Annotation (2006)
Pier Luigi Martelli, Piero Fariselli, Gianluca Tasco, Rita Casadio
New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β-barrel and all-α membrane proteins with high accuracy and a...
Andea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Eukaryotic Subcellular Localization DataBase collects the annotations of subcellular localization of eukaryotic proteomes. So far five proteomes have been processed and stored: Homo sapiens, Mus...
Marani, Paola, Wagner, Samuel, Baars, Louise, Genevaux, Pierre, De Gier, Jan-Willem, Nilsson, Ingmarie, ...
Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may...
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins (2006)
Amico, Mauro, Finelli, Michele, Rossi, Ivan, Zauli, Andrea, Elofsson, Arne, Viklund, Håkan, ...
The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating...
Marani, Paola, Wagner, Samuel, Baars, Louise, Genevaux, Pierre, De Gier, Jan-Willem, Nilsson, Ingmarie, ...
Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may...
BaCelLo: a balanced subcellular localization predictor (2006)
Pierleoni, Andrea, Martelli, Pier Luigi, Fariselli, Piero, Casadio, Rita
Motivation. The knowledge of the subcellular localization of a protein is fundamental for elucidating its function. It is difficult to determine the subcellular location for eukaryotic cells with...
Marani, Paola, Wagner, Samuel, Baars, Louise, Genevaux, Pierre, De Gier, Jan-Willem, Nilsson, Ingmarie, ...
Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may...
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,...
Fariselli, Piero, Martelli, Pier, Casadio, Rita
Abstract Background Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully applied to the problem of predicting...
Milanesi, Luciano, Petrillo, Mauro, Sepe, Leandra, Boccia, Angelo, D'Agostino, Nunzio, Passamano, Myriam, ...
Abstract Background Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular...
The posterior-Viterbi: a new decoding algorithm for hidden Markov models (2005)
Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita
Background: Hidden Markov models (HMM) are powerful machine learning tools successfully applied to problems of computational Molecular Biology. In a predictive task, the HMM is endowed with a...
Emidio Capriotti, Piero Fariselli, Rita Casadio
or structure
TRAMPLE: the transmembrane protein labelling (2005)
Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, ...
environment
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....
TRAMPLE: the transmembrane protein labelling environment (2005)
Fariselli, Piero, Finelli, Michele, Rossi, Ivan, Amico, Mauro, Zauli, Andrea, Martelli, Pier Luigi, ...
TRAMPLE (http://gpcr.biocomp.unibo.it/biodec/) is a web application server dedicated to the detection and the annotation of transmembrane protein sequences. TRAMPLE includes different...
Capriotti, Emidio, Fariselli, Piero, Casadio, Rita
I-Mutant2.0 is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. I-Mutant2.0 predictions are performed starting either...
Predicting protein stability changes from sequences using support vector machines (2005)
Capriotti, Emidio, Fariselli, Piero, Calabrese, Remo, Casadio, Rita
Motivation: The prediction of protein stability change upon mutations is key to understanding protein folding and misfolding. At present, methods are available to predict stability changes only when...
Anna Scotto D’Abusco, Rita Casadio, Gianluca Tasco, Laura Giangiacomo, Anna Giartosio, Valentina Calamia, ...
The recombinant amidase from the hyperthermophylic archaeon Sulfolobus solfataricus (SSAM) a signature amidase, was cloned, purified and characterized. The enzyme is active on a large number of...
Running Title: Prediction of functional and structural residues (2004)
Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, ...
Key words: evolutionary conservation, evolution rate, surface accessibility prediction, bestrophin Motivation: ConSeq is a web server for the identification of biologically important residues in...
Berezin, Carine, Glaser, Fabian, Rosenberg, Josef, Paz, Inbal, Pupko, Tal, Fariselli, Piero, ...
Motivation: ConSeq is a web server for the identification of biologically important residues in protein sequences. Functionally important residues that take part, e.g. in ligand binding and...
Capriotti, Emidio, Fariselli, Piero, Casadio, Rita
Motivation: One important requirement for protein design is to be able to predict changes of protein stability upon mutation. Different methods addressing this task have been described and their...
Berezin, Carine, Glaser, Fabian, Rosenberg, Josef, Paz, Inbal, Pupko, Tal, Fariselli, Piero, ...
Motivation: ConSeq is a web server for the identification of biologically important residues in protein sequences. Functionally important residues that take part, e.g. in ligand binding and...
Berezin, Carine, Glaser, Fabian, Rosenberg, Josef, Paz, Inbal, Pupko, Tal, Fariselli, Piero, ...
Motivation: ConSeq is a web server for the identification of biologically important residues in protein sequences. Functionally important residues that take part, e.g. in ligand binding and...
the prediction of all-alpha membrane proteins (2003)
Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Vol. 19 Suppl. 1 2003, pages i205–i211
The 4th Bologna Winter School: Hot Topics in Structural Genomics (2003)
The 4th Bologna Winter School on Biotechnologies was held on 9–15 February 2003 at the University of Bologna, Italy, with the specific aim of discussing recent developments in bioinformatics. The...
The Prediction of Membrane Protein Structure and Genome Structural Annotation (2003)
Pier Luigi Martelli, Piero Fariselli, Gianluca Tasco, Rita Casadio
New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β-barrel and all-α membrane proteins with high accuracy and a low rate of...
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites (2003)
Fariselli, Piero, Finocchiaro, Giacomo, Casadio, Rita
Summary: SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting...
Casadio, Rita, Fariselli, Piero, Finocchiaro, Giacomo, Martelli, Pier Luigi
We address the problem of clustering the whole protein content of genomes into three different categories—globular, all-α, and all-β membrane proteins—with the aim of fishing new membrane...
In silico prediction of the structure of membrane proteins: Is it feasible? (2003)
Casadio, Rita, Fariselli, Piero, Martelli, Pier Luigi
In the ‘omic’ era, hundreds of genomes are available for protein sequence analysis, and some 30 per cent of all sequences are of membrane proteins. Unlike globular proteins, a 3D model for...
Fariselli, Piero, Finelli, Michele, Marchignoli, Davide, Martelli, Pier Luigi, Rossi, Ivan, Casadio, Rita
Motivation: A problem in predicting the topography of transmembrane proteins is the optimal localization of the transmembrane segments along the protein sequences, provided that each residue is...
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins (2003)
Martelli, Pier Luigi, Fariselli, Piero, Casadio, Rita
Motivation: All-alpha membrane proteins constitute a functionally relevant subset of the whole proteome. Their content ranges from about 10 to 30% of the cell proteins, based on sequence...
Prediction of coordination number and relative solvent accessibility in proteins (2002)
Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, Rita Casadio
Irvine. To whom all correspondence should be addressed.
Prediction of Coordination Number and (2002)
Relative Solvent Accessibility, Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, Rita Casadio
Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and in...
Access the most recent version at doi: 10.1110/ps.0223603 References (2002)
Rita Casadio, Piero Fariselli, Giacomo Finocchiaro, Pier Luigi Martelli, Email Alerting, Rita Casadio, ...
Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria
Casadio, Rita, Martelli, Pier Luigi, Giordano, Antonietta, Rossi, Mosè, Raia, Carlo A.
We describe the computation of a model of the thermophilic NAD-dependent homotetrameric alcohol dehydrogenase from the archaeon Sulfolobus solfataricus (SsADH). Modeling is based on the knowledge...
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy (2002)
Martelli, Pier Luigi, Fariselli, Piero, Malaguti, Luca, Casadio, Rita
The task of predicting the cysteine-bonding state in proteins starting from the residue chain is addressed by implementing a new hybrid system that combines a neural network and a hidden Markov model...
Martelli, Pier Luigi, Fariselli, Piero, Krogh, Anders, Casadio, Rita
Motivation: Membrane proteins are an abundant and functionally relevant subset of proteins that putatively include from about 15 up to 30% of the proteome of organisms fully sequenced. These...
Martelli, Pier Luigi, Fariselli, Piero, Malaguti, Luca, Casadio, Rita
A hybrid system (hidden neural network) based on a hidden Markov model (HMM) and neural networks (NN) was trained to predict the bonding states of cysteines in proteins starting from the residue...
Gianluca Pollastri, Pierre Baldi, Pietro Fariselli, Rita Casadio
Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an...
Prediction of disulfide connectivity in proteins (2001)
Fariselli, Piero, Casadio, Rita
Motivation: A major problem in protein structure predictionis the correct location of disulfide bridges in cysteine-rich proteins. In protein-folding prediction, the location of disulfide bridges can...
Pollastri, Gianluca, Baldi, Pierre, Fariselli, Pietro, Casadio, Rita
Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an...
RCNPRED: prediction of the residue co-ordination numbers in proteins (2001)
Fariselli, Piero, Casadio, Rita
Summary: The RCNPRED server implements a neural network-based method to predict the co-ordination numbers of residues starting from the protein sequence. Using evolutionary information as input,...
Jacoboni, Irene, Martelli, Pier Luigi, Fariselli, Piero, De Pinto, Vito, Casadio, Rita
A method based on neural networks is trained and tested on a nonredundant set of &bgr;-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the...
Prediction of contact maps with neural networks and correlated mutations (2001)
Fariselli, Piero, Olmea, Osvaldo, Valencia, Alfonso, Casadio, Rita
Contact maps of proteins are predicted with neural network-based methods, using as input codings of increasing complexity including evolutionary information, sequence conservation, correlated...
P Fariselli, A Bottoni, F Bernardi, R Casadio, Email Alerting, Piero Fariselli, ...
Quantum mechanical analysis of oxygenated and deoxygenated states of hemocyanin: theoretical clues for a plausible allosteric model of oxygen binding
Topology prediction for helical transmembrane proteins at 86% accuracy (1996)
Burkhard Rost, Piero Fariselli, Rita Casadio
Previously, we introduced a neural network system predicting locations of transmembrane helices based on evolutionary profiles (PHDhtm, (Rost et al., 1995). Here, we describe an improvement and an...
Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming (1996)
Burkhard Rost, Rita Casadio, Piero Fariselli
For transmembrane proteins experimental determina-tion of three-dimensional structure is problematic. However, membrane proteins have important impact for molecular biology in general, and for drug...
Fariselli, Piero, Casadio, Rita
In this paper we describe a microcomputer program (HTP) for predicting the location and orientation of α-helical transmemhrane segments in integral membrane proteins. HTP is a neural network-based...
Transmembrane helices predicted at 95% accuracy (1995)
Burkhard Rost, Rita Casadio, Piero Fariselli, Chris Sander
We describe a neural network system that predicts the locations of transmembrane helices in integral membrane proteins. By using evolutionary information as input to the network system, the method...
Vivarelli, Francesco, Giusti, Giuliano, Villani, Marco, Campanini, Renato, Fariselli, Piero, Compiani, Mario, ...
In this work we describe a parallel system consisting of feed-forward neural networks supervised by a local genetic algorithm. The system is implemented in a transputer architecture and is used to...
An entropy criterion to detect minimally frustrated intermediates in native proteins
Compiani, Mario, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita
The analysis of the information flow in a feed-forward neural network suggests that the output of the network can be used to compute a structural entropy for the sequence-to-secondary structure...
Menotti, Laura, Casadio, Rita, Bertucci, Carlo, Lopez, Marc, Campadelli-Fiume, Gabriella
By analogy with its human nectin1 counterpart, murine nectin1 serves as a cellular receptor for the entry of herpes simplex virus (HSV) into murine cells. HSV entry mediated by either receptor is...
Gianni, Tatiana, Martelli, Pier Luigi, Casadio, Rita, Campadelli-Fiume, Gabriella
Human herpesviruses enter cells by fusion with target membranes, a process that requires three conserved glycoproteins: gB, gH, and gL. How these glycoproteins execute fusion is unknown. Neural...
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
Capriotti, Emidio, Fariselli, Piero, Casadio, Rita
I-Mutant2.0 is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. I-Mutant2.0 predictions are performed starting either...
TRAMPLE: the transmembrane protein labelling environment
Fariselli, Piero, Finelli, Michele, Rossi, Ivan, Amico, Mauro, Zauli, Andrea, Martelli, Pier Luigi, ...
TRAMPLE () is a web application server dedicated to the detection and the annotation of transmembrane protein sequences. TRAMPLE includes different state-of-the-art algorithms for the prediction of...
Transglutaminases: nature's biological glues.
Griffin, Martin, Casadio, Rita, Bergamini, Carlo M
Transglutaminases (Tgases) are a widely distributed group of enzymes that catalyse the post-translational modification of proteins by the formation of isopeptide bonds. This occurs either through...
Occhipinti, Emanuela, Martelli, Pier Luigi, Spinozzi, Francesco, Corsi, Federica, Formantici, Cristina, Molteni, Laura, ...
Sulfolobus solfataricus carboxypeptidase (CPSso) is a thermostable zinc-metalloenzyme with a Mr of 43,000. Taking into account the experimentally determined zinc content of one ion per subunit, we...
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
Amico, Mauro, Finelli, Michele, Rossi, Ivan, Zauli, Andrea, Elofsson, Arne, Viklund, Håkan, ...
The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating...
An entropy criterion to detect minimally frustrated intermediates in native proteins
Compiani, Mario, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita
The analysis of the information flow in a feed-forward neural network suggests that the output of the network can be used to compute a structural entropy for the sequence-to-secondary structure...
Menotti, Laura, Casadio, Rita, Bertucci, Carlo, Lopez, Marc, Campadelli-Fiume, Gabriella
By analogy with its human nectin1 counterpart, murine nectin1 serves as a cellular receptor for the entry of herpes simplex virus (HSV) into murine cells. HSV entry mediated by either receptor is...
Gianni, Tatiana, Martelli, Pier Luigi, Casadio, Rita, Campadelli-Fiume, Gabriella
Human herpesviruses enter cells by fusion with target membranes, a process that requires three conserved glycoproteins: gB, gH, and gL. How these glycoproteins execute fusion is unknown. Neural...
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
Capriotti, Emidio, Fariselli, Piero, Casadio, Rita
I-Mutant2.0 is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. I-Mutant2.0 predictions are performed starting either...
TRAMPLE: the transmembrane protein labelling environment
Fariselli, Piero, Finelli, Michele, Rossi, Ivan, Amico, Mauro, Zauli, Andrea, Martelli, Pier Luigi, ...
TRAMPLE () is a web application server dedicated to the detection and the annotation of transmembrane protein sequences. TRAMPLE includes different state-of-the-art algorithms for the prediction of...
Transglutaminases: nature's biological glues.
Griffin, Martin, Casadio, Rita, Bergamini, Carlo M
Transglutaminases (Tgases) are a widely distributed group of enzymes that catalyse the post-translational modification of proteins by the formation of isopeptide bonds. This occurs either through...
Occhipinti, Emanuela, Martelli, Pier Luigi, Spinozzi, Francesco, Corsi, Federica, Formantici, Cristina, Molteni, Laura, ...
Sulfolobus solfataricus carboxypeptidase (CPSso) is a thermostable zinc-metalloenzyme with a Mr of 43,000. Taking into account the experimentally determined zinc content of one ion per subunit, we...
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
Amico, Mauro, Finelli, Michele, Rossi, Ivan, Zauli, Andrea, Elofsson, Arne, Viklund, Håkan, ...
The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating...
eSLDB: eukaryotic subcellular localization database
Pierleoni, Andea, Martelli, Pier Luigi, Fariselli, Piero, Casadio, Rita
Eukaryotic Subcellular Localization DataBase collects the annotations of subcellular localization of eukaryotic proteomes. So far five proteomes have been processed and stored: Homo sapiens, Mus...
Milanesi, Luciano, Petrillo, Mauro, Sepe, Leandra, Boccia, Angelo, D'Agostino, Nunzio, Passamano, Myriam, ...
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
A computational approach for detecting peptidases and their specific inhibitors at the genome level
Bartoli, Lisa, Calabrese, Remo, Fariselli, Piero, Mita, Damiano G, Casadio, Rita
The implications of alternative splicing in the ENCODE protein complement
Tress, Michael L., Martelli, Pier Luigi, Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan Jaap, Yeats, Corin, ...
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological...
Marani, Paola, Wagner, Samuel, Baars, Louise, Genevaux, Pierre, De Gier, Jan-Willem, Nilsson, Ingmarie, ...
Many new Escherichia coli outer membrane proteins have recently been identified by proteomics techniques. However, poorly expressed proteins and proteins expressed only under certain conditions may...
A three-state prediction of single point mutations on protein stability changes
Capriotti, Emidio, Fariselli, Piero, Rossi, Ivan, Casadio, Rita
Casadio, Rita, Fariselli, Piero, Finocchiaro, Giacomo, Martelli, Pier Luigi
We address the problem of clustering the whole protein content of genomes into three different categories—globular, all-α, and all-β membrane proteins—with the aim of fishing new membrane...
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy
Martelli, Pier Luigi, Fariselli, Piero, Malaguti, Luca, Casadio, Rita
The task of predicting the cysteine-bonding state in proteins starting from the residue chain is addressed by implementing a new hybrid system that combines a neural network and a hidden Markov model...
Jacoboni, Irene, Martelli, Pier Luigi, Fariselli, Piero, De Pinto, Vito, Casadio, Rita
A method based on neural networks is trained and tested on a nonredundant set of β-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography...
The 4th Bologna Winter School: Hot Topics in Structural Genomics
The 4th Bologna Winter School on Biotechnologies was held on 9–15 February 2003 at the University of Bologna, Italy, with the specific aim of discussing recent developments in bioinformatics. The...
The Prediction of Membrane Protein Structure and Genome Structural Annotation
Martelli, Pier Luigi, Fariselli, Piero, Tasco, Gianluca, Casadio, Rita
New methods, essentially based on hidden Markov models (HMM) and neural networks (NN), can predict the topography of both β-barrel and all-α membrane proteins with high accuracy and a low rate of...
D’Abusco, Anna Scotto, Casadio, Rita, Tasco, Gianluca, Giangiacomo, Laura, Giartosio, Anna, Calamia, Valentina, ...
The recombinant amidase from the hyperthermophylic archaeon Sulfolobus solfataricus (SSAM) a signature amidase, was cloned, purified and characterized. The enzyme is active on a large number of...
Sequence-based feature prediction and annotation of proteins
Juncker, Agnieszka S, Jensen, Lars J, Pierleoni, Andrea, Bernsel, Andreas, Tress, Michael L, Bork, Peer, ...
The combination of prediction tools in complex workflows and pipelines facilitates prediction of protein features from sequence.
Predicting protein thermostability changes from sequence upon multiple mutations
Montanucci, Ludovica, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita
Motivation: A basic question in protein science is to which extent mutations affect protein thermostability. This knowledge would be particularly relevant for engineering thermostable enzymes. In...