Jain, S., Ranjan, P., Sengupta, D. and Naik, P.K. 2012. TpPred: A Tool for Hierarchical Prediction of Transport Proteins Using Cluster of Neural Networks and Sequence Derived Features. International Journal for Computational Biology. 1 (1), pp. 28-36.
| Title | TpPred: A Tool for Hierarchical Prediction of Transport Proteins Using Cluster of Neural Networks and Sequence Derived Features |
|---|---|
| Type | Journal article |
| Authors | Jain, S., Ranjan, P., Sengupta, D. and Naik, P.K. |
| Abstract | A top–down predictor, called TpPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1st layer of the prediction engine is for identifying a query protein as transport protein or not; the 2nd layer for the main functional class; and the 3rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 65% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. TpPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of transport proteins. TpPred is freely available to be use in-house as a standalone version and is accessible at http://www.juit.ac.in/attachments/tppred/Home.html. |
| Journal | International Journal for Computational Biology |
| Journal citation | 1 (1), pp. 28-36 |
| Year | 2012 |
| Publication dates | |
| Published | Jul 2012 |
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Interpretable semisupervised classifier for predicting cancer stages
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Machine learning in precision medicine
Sengupta, D. 2021. Machine learning in precision medicine. in: Kumar, P., Kumar, Y. and Tawhid, M.A. (ed.) Machine Learning, Big Data, and IoT for Medical Informatics Academic Press. pp. 405-419
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Grau, I., Sengupta, D., Garcia Lorenzo, M.M. and Nowe, A. 2020. An interpretable semi-supervised classifier using rough sets for amended self-labeling. IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2020). Glasgow, UK 19 - 24 Jul 2020 IEEE . https://doi.org/10.1109/fuzz48607.2020.9177549
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Grey-Box Model: An ensemble approach for addressing semi-supervised classification problems
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GEVACT: Genomic Variant Classifier Tool
Daneels, D., Grau, I., Sengupta, D., Bonduelle, M., Farid, D.M., Croes, D., Nowé, A. and Van Dooren, S. 2015. GEVACT: Genomic Variant Classifier Tool. BeSHG & NVHG First Joint Meeting “Genetics & Society”. Leuven, Belgium 04 - 05 Feb 2016
CliniPhenome: Clinical and Phenotypic Annotation Database
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GeVaCT: Genomic Variant Classifier Tool
Grau, I., Daneels, D., Van Dooren, S., Bonduelle , M., Farid, D.M., Croes, D., Nowé, A. and Sengupta, D. 2015. GeVaCT: Genomic Variant Classifier Tool. 10th Benelux Bioinformatics Conference. University of Antwerp, Belgium 07 - 08 Dec 2015
CliniPhenome: Clinical and Phenotypic Annotation Database
Sengupta, D., Croes, D., Van Dooren, S., Bonduelle, M. and Nowe, A. 2015. CliniPhenome: Clinical and Phenotypic Annotation Database. 2nd International Conference on Health Informatics & Technology. Valencia, Spain 27 - 29 Jul 2015 OMICS Publishing Group.
Benchmarking pre-processing and batch effect removal methods for Insilico DB: Genomics Big Data Infrastructure
De Clerck, Q., Nowe, A., Coletta, A. and Sengupta, D. 2014. Benchmarking pre-processing and batch effect removal methods for Insilico DB: Genomics Big Data Infrastructure. 9th Benelux Bioinformatics Conference (BBC 2014). Novotel-Kirchberg, Luxembourg 08 - 09 Dec 2014
Homology Modeling of Bacteriocins: From sequence alignments to structural models
Atri, P., Sengupta, D., Verma, S., Ali, S. and Dey, G. 2014. Homology Modeling of Bacteriocins: From sequence alignments to structural models. International Journal of Scientific & Engineering Research. 5 (5), pp. 123-126.
Association rule mining based study for identification of clinical parameters akin to occurrence of brain tumor
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Design of dimensional model for clinical data storage and analysis
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SN algorithm: analysis of temporal clinical data for mining periodic patterns and impending augury
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Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix
Pathak, P., Naik, P.K., Sengupta, D., Singh, S.K. and Tandon, C. 2011. Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix. Journal of Biomedical Science and Engineering. 4 (9), pp. 591-598. https://doi.org/10.4236/jbise.2011.49075
Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues
Sengupta, D., Verma, D. and Naik, P.K. 2008. Docking-MM-GB/SA and ADME screening of HIV-1 NNRTI inhibitor: Nevirapine and its analogues. In Silico Biology. 8 (3-4), pp. 275-289.
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Sengupta, D. 2007. Binding Modes, binding Affinities and ADME Screening of HIV-1 NNRTI Inhibitor: Efavirnez and its analogues. Online Journal of Bioinformatics. 8 (1), pp. 99-114.
In-silico TAT-PTD prediction for cell penetrating peptides
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Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: Screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
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Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
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Clustering of HIV-I Subtype: Study of Molecular Diversity using Phylogenetic Analysis
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