SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
Identifieur interne : 004D71 ( Main/Exploration ); précédent : 004D70; suivant : 004D72SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
Auteurs : Gaurav Sachdeva [Inde] ; Kaushal Kumar [Inde] ; Preti Jain [Inde] ; Srinivasan Ramachandran [Inde]Source :
- Bioinformatics : (Oxford. Print) [ 1367-4803 ] ; 2005.
Descripteurs français
- KwdFr :
- Adhésines bactériennes (), Adhésines bactériennes (métabolisme), Algorithmes, Alignement de séquences (), Analyse de séquence de protéine (), Animaux, Humains, Isoformes de protéines (), Isoformes de protéines (métabolisme), Logiciel, Modèles biologiques, Modèles chimiques, Modèles statistiques, Relation structure-activité, Similitude de séquences d'acides aminés.
- MESH :
- métabolisme : Adhésines bactériennes, Isoformes de protéines.
- Pascal (Inist)
- Adhésines bactériennes, Algorithmes, Alignement de séquences, Analyse de séquence de protéine, Animaux, Humains, Isoformes de protéines, Logiciel, Modèles biologiques, Modèles chimiques, Modèles statistiques, Prédiction, Adhésine, Protéine, Relation structure-activité, Réseau neuronal, Bioinformatique, Similitude de séquences d'acides aminés.
- Wicri :
- topic : Logiciel.
English descriptors
- KwdEn :
- Adhesin, Adhesins, Bacterial (chemistry), Adhesins, Bacterial (metabolism), Algorithms, Animals, Bioinformatics, Humans, Models, Biological, Models, Chemical, Models, Statistical, Neural Networks, Computer, Neural network, Prediction, Protein, Protein Isoforms (chemistry), Protein Isoforms (metabolism), Sequence Alignment (methods), Sequence Analysis, Protein (methods), Sequence Homology, Amino Acid, Software, Structure-Activity Relationship.
- MESH :
- chemical , chemistry : Adhesins, Bacterial, Protein Isoforms.
- chemical , metabolism : Adhesins, Bacterial, Protein Isoforms.
- methods : Sequence Alignment, Sequence Analysis, Protein.
- Algorithms, Animals, Humans, Models, Biological, Models, Chemical, Models, Statistical, Neural Networks, Computer, Sequence Homology, Amino Acid, Software, Structure-Activity Relationship.
Abstract
Motivation: The adhesion of microbial pathogens to host cells is mediated by adhesins. Experimental methods used for characterizing adhesins are time-consuming and demand large resources. The availability of specialized software can rapidly aid experimenters in simplifying this problem. We have employed 105 compositional properties and artificial neural networks to develop SPAAN, which predicts the probability of a protein being an adhesin (Pad). Results: SPAAN had optimal sensitivity of 89% and specificity of 100% on a defined test set and could identify 97.4% of known adhesins at high Pad value from a wide range of bacteria. Furthermore, SPAAN facilitated improved annotation of several proteins as adhesins. Novel adhesins were identified in 17 pathogenic organisms causing diseases in humans and plants. In the severe acute respiratory syndrome (SARS) associated human corona virus, the spike glycoprotein and nsps (nsp2, nsp5, nsp6 and nsp7) were identified as having adhesin-like characteristics. These results offer new lead for rapid experimental testing.
Affiliations:
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Le document en format XML
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Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road</s1><s2>Delhi 110 007</s2><s3>IND</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ></inist:fA14><country>Inde</country><wicri:noRegion>Delhi 110 007</wicri:noRegion></affiliation></author><author><name sortKey="Ramachandran, Srinivasan" sort="Ramachandran, Srinivasan" uniqKey="Ramachandran S" first="Srinivasan" last="Ramachandran">Srinivasan Ramachandran</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>G. N. Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road</s1><s2>Delhi 110 007</s2><s3>IND</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ></inist:fA14><country>Inde</country><wicri:noRegion>Delhi 110 007</wicri:noRegion></affiliation></author></analytic><series><title level="j" type="main">Bioinformatics : (Oxford. 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Print)</title><title level="j" type="abbreviated">Bioinformatics : (Oxf., Print)</title><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adhesin</term><term>Adhesins, Bacterial (chemistry)</term><term>Adhesins, Bacterial (metabolism)</term><term>Algorithms</term><term>Animals</term><term>Bioinformatics</term><term>Humans</term><term>Models, Biological</term><term>Models, Chemical</term><term>Models, Statistical</term><term>Neural Networks, Computer</term><term>Neural network</term><term>Prediction</term><term>Protein</term><term>Protein Isoforms (chemistry)</term><term>Protein Isoforms (metabolism)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, Protein (methods)</term><term>Sequence Homology, Amino Acid</term><term>Software</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adhésines bactériennes ()</term><term>Adhésines bactériennes (métabolisme)</term><term>Algorithmes</term><term>Alignement de séquences ()</term><term>Analyse de séquence de protéine ()</term><term>Animaux</term><term>Humains</term><term>Isoformes de protéines ()</term><term>Isoformes de protéines (métabolisme)</term><term>Logiciel</term><term>Modèles biologiques</term><term>Modèles chimiques</term><term>Modèles statistiques</term><term>Relation structure-activité</term><term>Similitude de séquences d'acides aminés</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Adhesins, Bacterial</term><term>Protein Isoforms</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Adhesins, Bacterial</term><term>Protein Isoforms</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Adhésines bactériennes</term><term>Isoformes de protéines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Humans</term><term>Models, Biological</term><term>Models, Chemical</term><term>Models, Statistical</term><term>Neural Networks, Computer</term><term>Sequence Homology, Amino Acid</term><term>Software</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Adhésines bactériennes</term><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de séquence de protéine</term><term>Animaux</term><term>Humains</term><term>Isoformes de protéines</term><term>Logiciel</term><term>Modèles biologiques</term><term>Modèles chimiques</term><term>Modèles statistiques</term><term>Prédiction</term><term>Adhésine</term><term>Protéine</term><term>Relation structure-activité</term><term>Réseau neuronal</term><term>Bioinformatique</term><term>Similitude de séquences d'acides aminés</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: The adhesion of microbial pathogens to host cells is mediated by adhesins. Experimental methods used for characterizing adhesins are time-consuming and demand large resources. The availability of specialized software can rapidly aid experimenters in simplifying this problem. We have employed 105 compositional properties and artificial neural networks to develop SPAAN, which predicts the probability of a protein being an adhesin (Pad). Results: SPAAN had optimal sensitivity of 89% and specificity of 100% on a defined test set and could identify 97.4% of known adhesins at high Pad value from a wide range of bacteria. Furthermore, SPAAN facilitated improved annotation of several proteins as adhesins. Novel adhesins were identified in 17 pathogenic organisms causing diseases in humans and plants. In the severe acute respiratory syndrome (SARS) associated human corona virus, the spike glycoprotein and nsps (nsp2, nsp5, nsp6 and nsp7) were identified as having adhesin-like characteristics. These results offer new lead for rapid experimental testing.</div></front></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Sachdeva, Gaurav" sort="Sachdeva, Gaurav" uniqKey="Sachdeva G" first="Gaurav" last="Sachdeva">Gaurav Sachdeva</name></noRegion><name sortKey="Jain, Preti" sort="Jain, Preti" uniqKey="Jain P" first="Preti" last="Jain">Preti Jain</name><name sortKey="Kumar, Kaushal" sort="Kumar, Kaushal" uniqKey="Kumar K" first="Kaushal" last="Kumar">Kaushal Kumar</name><name sortKey="Ramachandran, Srinivasan" sort="Ramachandran, Srinivasan" uniqKey="Ramachandran S" first="Srinivasan" last="Ramachandran">Srinivasan Ramachandran</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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