Proteases are responsible for a number of fundamental cellular activities, such as protein turnover and defense against pathogenic organisms. non redundant set of globular proteins can be improved by some percentage points with respect to that obtained with each method separately. More importantly, our method can then predict pairs of peptidases and interacting inhibitors, scoring a joint global accuracy of 99% with coverage for the positive cases (peptidase/inhibitor) close to 100% and a correlation coefficient of 0.91%. In this task the decision-tree approach outperforms the single methods. Conclusion The decision-tree can reliably classify protein sequences as peptidases or inhibitors, belonging to a certain class, and can provide a comprehensive list of possible interacting pairs of peptidase/inhibitor. This information can help the design of experiments to detect interacting peptidase/inhibitor complexes and can speed up the selection of possible interacting candidates, without searching for them separately and manually combining the obtained results. A web server specifically developed for annotating peptidases and their inhibitors (HIPPIE) is usually available at http://gpcr.biocomp.unibo.it/cgi/predictors/hippie/pred_hippie.cgi Background Peptidases (proteases) are proteolytic enzymes essential for the life of all organisms. The relevance of peptidases is usually proved by the fact that 2C5% of all genes encode for peptidases and/or their homologs irrespectively of the organism source [1]. In the SwissProt database [2] about 18% of sequences are annotated as “undergoing proteolytic processing”, and there are over 550 known and putative peptidases in the human genome. It is also worth noticing that more than 10% of the human peptidases are under investigation as drug targets [3]. Proteases are responsible for a number of fundamental cellular activities, such as protein turnover and defense against pathogenic organisms. Since the basic protease function is usually “protein digestion”, these proteins would be potentially dangerous in living organisms, if not fully controlled. This is one of the major reasons for the presence of their natural inhibitors inside the cell. All peptidases catalyze the same reaction, namely the hydrolysis of a peptide bond, but they are selective for the position of the substrate and also for the amino acid residues close to the bond that undergoes hydrolysis [4,5]. There are different classes of peptidases identified by the catalytic group involved in the hydrolysis of the peptide bond. However the majority of the peptidases can be assigned to one of the following four functional classes: ? Serine Peptidase ? Aspartic Peptidase PFE-360 (PF-06685360) ? Cysteine Peptidase ? Metallopeptidase In the serine and cysteine types the catalytic nucleophile can be the reactive group of the amino acid side chain, a hydroxyl group (serine peptidase) or a sulfhydryl group (cysteine peptidase). In aspartic and metallopeptidases the nucleophile is commonly “an activated water molecule”. In aspartic peptidases the side chains of aspartic residues directly bind the water molecule. In metallopeptidases one or two metal ions hold the water molecule in place and charged amino acid side chains are ligands for the metal ions. The metal may be zinc, cobalt or manganese, and a single metal ion is usually bound by three amino acid ligands [3]. Among the different ways to control their activity, the most important is usually through the interactions of the protein with other proteins, namely naturally occurring peptidase inhibitors. Peptidase inhibitors can or cannot be specific for a certain group of catalytic reactions. In general there are two kinds of interactions between peptidases and their inhibitors: the first one is an irreversible process of “trapping”, leading to a stable peptidase-inhibitor complex; the second one is a reversible process in which there is a tight binding reaction without any chemical bond formation [4,6-8]. A shift of interest towards mode of conversation of protein inhibitors with their targets is due to the possibility of designing new synthetic inhibitors. The research is usually driven by the many potential applications in medicine, agriculture and biotechnology. In the last years, an invaluable source of information about proteases and their inhibitors has PFE-360 (PF-06685360) been made available through the MEROPS database [9], so that it is possible to search for known peptidase sequences (or structures) or peptidase-inhibitor sequences (or structures). Exploiting this source, in this paper we address the problem of relating a peptidase sequence (or inhibitor) with sequences that can putatively but reliably inhibit it (or proteases that can be inhibited by it). To this aim we implemented a method that first and reliably discriminates whether a given sequence is usually a peptidase or a peptidase-inhibitor, and afterwards gives a list of its.The basic peptidase function is “protein digestion” and this can be potentially dangerous in living organisms when it is not strictly controlled BTD by specific inhibitors. eventually listing all possible predicted ligands (peptidases and/or inhibitors). Results We show that by adopting a decision-tree approach the accuracy of PROSITE and HMMER in detecting separately the four major peptidase types (Serine, Aspartic, Cysteine and Metallo- Peptidase) and their inhibitors among a non redundant set of globular proteins can be improved by some percentage points with respect to that obtained with each method separately. More importantly, our method can then predict pairs of peptidases and interacting inhibitors, scoring a joint global accuracy of 99% with coverage for the positive cases (peptidase/inhibitor) close to 100% and a correlation coefficient of 0.91%. In this task the decision-tree approach outperforms the single methods. Conclusion The decision-tree can reliably classify protein sequences as peptidases or inhibitors, belonging to a certain class, and can provide a comprehensive list of possible interacting pairs of peptidase/inhibitor. This information can help the design of experiments to detect interacting peptidase/inhibitor complexes and can speed up the selection of possible interacting candidates, without searching for them separately and manually combining the obtained results. A web server specifically developed for annotating peptidases and their inhibitors (HIPPIE) is available at http://gpcr.biocomp.unibo.it/cgi/predictors/hippie/pred_hippie.cgi Background Peptidases (proteases) are proteolytic enzymes essential for the life of all organisms. The relevance of peptidases is proved by the fact that 2C5% of all genes encode for peptidases and/or their homologs irrespectively of the organism source [1]. In the SwissProt database [2] about 18% of sequences are annotated as “undergoing proteolytic processing”, and there are over 550 known and putative peptidases in the human genome. It is also worth noticing that more than 10% of the human peptidases are under investigation as drug targets [3]. Proteases are responsible for a number of fundamental cellular activities, such as protein turnover and defense against pathogenic organisms. Since the basic protease function is “protein digestion”, these proteins would be potentially dangerous in living organisms, if not fully controlled. This is one of the major reasons for the presence of their natural inhibitors inside the cell. All peptidases catalyze the same reaction, namely the hydrolysis of a peptide bond, but they are selective for the position of the substrate and also for the amino acid residues close to the bond that undergoes hydrolysis [4,5]. There are different classes of peptidases identified by the catalytic group involved in the hydrolysis of the peptide bond. However the majority of the peptidases can be assigned to one of the following four functional classes: ? Serine Peptidase ? Aspartic Peptidase ? Cysteine Peptidase ? Metallopeptidase In the serine and cysteine types the catalytic nucleophile can be the reactive group of the amino acid side chain, a hydroxyl group (serine peptidase) or a sulfhydryl group (cysteine peptidase). In aspartic and metallopeptidases the nucleophile is commonly “an activated water molecule”. In aspartic peptidases the side chains of aspartic residues directly bind the water molecule. In metallopeptidases one or two metal ions hold the water molecule in place and charged amino acid side chains are ligands for the metal ions. The metal may be zinc, cobalt or manganese, and a single metal ion is usually bound by three amino acid ligands [3]. Among the different ways to control their activity, the most important is through the interactions of the protein with other proteins, namely naturally occurring peptidase inhibitors. Peptidase inhibitors can or cannot be PFE-360 (PF-06685360) specific for a certain group of catalytic reactions. In general there are two kinds of interactions between peptidases and their inhibitors: the first one is an irreversible process of “trapping”, leading to a stable peptidase-inhibitor complex; the second one is a reversible process in which.Among the different ways to control their activity, the most important is through the interactions of the protein with other proteins, namely naturally occurring peptidase inhibitors. scoring a joint global accuracy of 99% with coverage for the positive cases (peptidase/inhibitor) close to 100% and a correlation coefficient of 0.91%. In this task the decision-tree approach outperforms the single methods. Conclusion The decision-tree can reliably classify protein sequences as peptidases or inhibitors, belonging to a certain class, and can provide a comprehensive list of possible interacting pairs of peptidase/inhibitor. This information can help the design of experiments to detect interacting peptidase/inhibitor complexes and can speed up the selection of possible interacting candidates, without searching for them separately and manually combining the obtained results. A web server specifically developed for annotating peptidases and their inhibitors (HIPPIE) is available at http://gpcr.biocomp.unibo.it/cgi/predictors/hippie/pred_hippie.cgi Background Peptidases PFE-360 (PF-06685360) (proteases) are proteolytic enzymes essential for the life of all organisms. The relevance of peptidases is proved by the fact that 2C5% of all genes encode for peptidases and/or their homologs irrespectively of the organism source [1]. In the SwissProt database [2] about 18% of sequences are annotated as “undergoing proteolytic processing”, and there are over 550 known and putative peptidases in the human genome. It is also worth noticing that more than 10% of the human peptidases are under investigation as drug targets [3]. Proteases are responsible for a number of fundamental cellular activities, such as protein turnover and defense against pathogenic organisms. Since the basic protease function is “protein digestion”, these proteins would be potentially dangerous in living organisms, if not fully controlled. This is one of the major reasons for the presence of their natural inhibitors inside the cell. All peptidases catalyze the same reaction, namely the hydrolysis of a peptide bond, but they are selective for the position of the substrate and also for the amino acid residues close to the bond that undergoes hydrolysis [4,5]. There are different classes of peptidases identified by the catalytic group involved in the hydrolysis of the peptide bond. However the majority of the peptidases can be assigned to one of the following four functional classes: ? Serine Peptidase ? Aspartic Peptidase ? Cysteine Peptidase ? Metallopeptidase In the serine and cysteine types the catalytic nucleophile can be the reactive group of the amino acid side chain, a hydroxyl group (serine peptidase) or a sulfhydryl group (cysteine peptidase). In aspartic and metallopeptidases the nucleophile is commonly “an activated water molecule”. In aspartic peptidases the side chains of aspartic residues directly bind the water molecule. In metallopeptidases one or two metal ions hold the water molecule in place and charged amino acid side chains are ligands for the metal ions. The metal may be zinc, cobalt or manganese, and a single metal ion is usually bound by three amino acid ligands [3]. Among the different ways to control their activity, the most important is through the interactions of the protein with other proteins, namely naturally occurring peptidase inhibitors. Peptidase inhibitors can or cannot be specific for a certain group of catalytic reactions. In general PFE-360 (PF-06685360) there are two kinds of interactions between peptidases and their inhibitors: the first one is an irreversible process of “trapping”, leading to a stable peptidase-inhibitor complex; the second.