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A Recurrent Neural Network Linear B-Epitope Predictor: BIRUNI

Azra Abidi
2018 Southeast Europe Journal of Soft Computing  
Lastly, the ABCpred prediction tool is an artificial neural network-based B cell epitope prediction server that recognizes that B cell epitopes have varying lengths (5 to 20 residues).  ...  To predict B in an antigenic sequence, Jordan recurrent neural network ( found to besuccessful.  ... 
doi:10.21533/scjournal.v7i2.165 fatcat:lc4kcfcxdffqvboy4nuhfqcwkm

Drug Design for Malaria with Artificial Intelligence (AI) [chapter]

Bhaswar Ghosh, Soham Choudhuri
2021 Plasmodium Species and Drug Resistance [Working Title]  
This poses a serious threat to efficacy of the treatments and continuing discovery of new drug is necessary to tackle the situation, especially due to failure in designing an effective vaccine.  ...  People are now trying to design new drugs for malaria using AI technologies which can substantially reduce the time and cost required in classical drug discovery programs.  ...  For protein-ligand interactions, neural network-based scoring mechanism [64] ODDT A robust chemoinformatics and molecular modelling toolkit for use [65] ORGANIC An powerful method for molecular generation  ... 
doi:10.5772/intechopen.98695 fatcat:4ikjazbbbbgtvlwmgeq5fg54p4

On the Accuracies of Sequence Based Linear B Cell Epitope Predictors

Azra Abidi, Mehmet Can
2018 Southeast Europe Journal of Soft Computing  
The accuracy of online tools employed in attempts to predict B epitopes based on sequence are very poor.  ...  In order to improve the accuracy of these predictions it is essential to design algorithms from the features achieved in wet lab in vivo experimental models.  ...  Lastly, the ABCpred prediction tool is an artificial neural network-based B cell epitope prediction server that recognizes that B cell epitopes have varying lengths (5 to 20 residues).  ... 
doi:10.21533/scjournal.v6i2.142 fatcat:wbclj632pjh4heagdyqoeypmpq

A review on Machine Learning approaches and trends in drug discovery

Paula Carracedo-Reboredo, Jose Linares-Blanco, Nereida Rodriguez-Fernandez, Francisco Cedron, Francisco J. Novoa, Adrian Carballal, Victor Maojo, Alejandro Pazos, Carlos Fernandez-Lozano
2021 Computational and Structural Biotechnology Journal  
Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies.  ...  This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.  ...  Artificial Neural Networks To be able to talk about ANN, we must first talk about the artificial neuron, which will be a functional element of the network which receives information from other elements  ... 
doi:10.1016/j.csbj.2021.08.011 pmid:34471498 pmcid:PMC8387781 fatcat:s5pwhypudfehbotkrofqgbq33m

The Application of Biomedical Engineering Techniques to the Diagnosis and Management of Tropical Diseases: A Review

Fatimah Ibrahim, Tzer Thio, Tarig Faisal, Michael Neuman
2015 Sensors  
lab-on-chip and micro-/nano-fluidic platforms and medical support systems such as artificial intelligence clinical support systems are discussed.  ...  The paper also reviewed the novel clinical diagnosis and management systems using artificial intelligence and bioelectrical impedance techniques for dengue clinical applications.  ...  Self-Organizing Map (SOM) The self-organizing map (SOM) is an unsupervised neural network that is considered as one of the most powerful aids for visualizing, analyzing, and understanding the complexity  ... 
doi:10.3390/s150306947 pmid:25806872 pmcid:PMC4435123 fatcat:j7l22yictnce5e7voxqiubpqry

A Predictive Model to Classify Undifferentiated Fever Cases Based on Twenty-Four-Hour Continuous Tympanic Temperature Recording

Pradeepa H. Dakappa, Keerthana Prasad, Sathish B. Rao, Ganaraja Bolumbu, Gopalkrishna K. Bhat, Chakrapani Mahabala
2017 Journal of Healthcare Engineering  
The aim of the study was to record and analyze a 24-hour continuous tympanic temperature and evaluate its utility in the diagnosis of undifferentiated fevers.  ...  Temperature data were preprocessed and various signal characteristic features were extracted and trained in classification machine learning algorithms using MATLAB software.  ...  Acknowledgments This research was supported by the Kasturba Medical College and Hospitals, Manipal University, Mangaluru, Karnataka, India.  ... 
doi:10.1155/2017/5707162 pmid:29359037 pmcid:PMC5735677 fatcat:ggylbk757jgpzosa4abmczdzny

In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19

Andrés López-Cortés, Patricia Guevara-Ramírez, Nikolaos C. Kyriakidis, Carlos Barba-Ostria, Ángela León Cáceres, Santiago Guerrero, Esteban Ortiz-Prado, Cristian R. Munteanu, Eduardo Tejera, Doménica Cevallos-Robalino, Ana María Gómez-Jaramillo, Katherine Simbaña-Rivera (+14 others)
2021 Frontiers in Pharmacology  
Then, we performed fully connected deep neural networks to find the best multitask classification model to predict the activity of 10,672 drugs, obtaining several approved drugs, compounds under investigation  ...  , single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19.Results: We screened 1,584 high-confidence immune  ...  CM and ET performed the artificial neural networks. AL, SG, EO, DC, AG, KS, AG, GP, SM, JG, AZ, YP, AC, LP, CP, JB, AQ, NV, LQ, and CP gave valuable scientific input and did data curation.  ... 
doi:10.3389/fphar.2021.598925 pmid:33716737 pmcid:PMC7952300 fatcat:ee2tpbfhnjctvovmdkd5xt2vqu

Screening and characterization of hypothetical proteins of Plasmodium falciparum as novel vaccine candidates in the fight against malaria using reverse vaccinology

Claire Aguttu, Brenda Apio Okech, Ambrose Mukisa, George William Lubega
2021 Journal of Genetic Engineering and Biotechnology  
(Mdv-1) at 0.645, and XP_001351047.1 with an uncharacterized protein (MAL8P1.53) at 0.400.  ...  Among the 5 extracellular proteins, 3 were predicted to be antigenic by VaxiJen (score ≥ 0.5) and had negative GRAVY values ranging from − 1.156 to − 0.440.  ...  Acknowledgements Special thanks are due to Dr. Mulindwa Julius and Dr. Isanga Joel for proofreading and English editing of the manuscript.  ... 
doi:10.1186/s43141-021-00199-y fatcat:lojlawhc5rabvgl45ag7i5c3ya

Synthetic Biology and Personalized Medicine

K.K. Jain
2013 Medical Principles and Practice  
Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs  ...  The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already  ...  networks in living organisms.  ... 
doi:10.1159/000341794 pmid:22907209 pmcid:PMC5586729 fatcat:n53kw3i3pjcs5bvygcdgyjtqou

Cough Classification for COVID-19 based on audio mfcc features using Convolutional Neural Networks

Vipin Bansal, Gaurav Pahwa, Nirmal Kannan
2020 2020 IEEE International Conference on Computing, Power and Communication Technologies (GUCON)  
The two approaches proposed in this paper are based on mfcc features and spectrogram images as input to CNN network.  ...  With symptoms like other respiratory illnesses, dry cough, fever and fatigue, it is challenging to classify probable Covid infection with no Covid data available yet.  ...  Authors would like to thank Dinesh Singh and Naveen Kumar S for his support and guidance. We are grateful to Andrew Koubatis and Nycil George for reviewing the paper and providing genuine feedback.  ... 
doi:10.1109/gucon48875.2020.9231094 fatcat:l6hutnx62vcpdfs34rjdadmf64

Anticancer Activity And Drug Likeliness Of Quinoline Through Insilico Docking Against Cervical And Liver Cancer Receptors

M.P.Santhi, G.Bupesh*
2016 Zenodo  
Quinoline is a versatile heterocyclic compound used to anti-inflammatory and anti- malarial properties.  ...  It is an imperative and striking focus for anticancer medication advancement and disclosure. Biophytum sensitivum is a medicinal plant rich in quinoline and amentoflavone.  ...  Acknowledgement The Authors would like to thank Director, King Institute of Preventive Medicine and Research, India for their support towards providing necessary infrastructure to carry out this study.  ... 
doi:10.5281/zenodo.157164 fatcat:s7hwrmzngnc33a37paktbh2dgm

Topological network measures for drug repositioning

Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter
2020 Briefings in Bioinformatics  
Computational approaches are significantly contributing to these efforts, of which, network-based methods play a key role.  ...  Various structural (topological) network measures have thereby contributed to uncovering unintuitive functional relationships and repositioning candidates in drug-disease and other networks.  ...  A prediction may also be an artifact due to the use of limited or conflicting data, or a single data-type.  ... 
doi:10.1093/bib/bbaa357 pmid:33348366 pmcid:PMC8294518 fatcat:zc2wwglvxbeb3fxxjypukchpzq

Integrating a Trimble Recon X 400 MHz Intel PXA255 Xscale CPU® Mobile Field Data Collection System Using Differentially Corrected Global Positioning System Technology and a Real-Time Bidirectional Actionable Platform within an ArcGIS Cyberenvironment for Implementing Mosquito Control

Benjamin G. Jacob, Robert J. Novak
2014 Advances in Remote Sensing  
Linkages were developed between the DSSAT Cropping System Model (CSM) and the PROSAIL radiative transfer model (CSM-PROSAIL) and between the DSSAT-CSM and an empirical model relating vegetation LULC parameter  ...  The outcome of the model inversion procedure was influenced by the timing and availability of remote sensing data, the spectral resolution of the data, the types of models implemented, and the choice of  ...  back propagation artificial neural network (ANN) in IDRISI.  ... 
doi:10.4236/ars.2014.33012 fatcat:sg5srenclnatlilciuy3pv3nx4

Towards reproducible computational drug discovery

Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
2020 Journal of Cheminformatics  
It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.  ...  In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations  ...  The authors would also like to thank Dr. Sirarat Sarntivijai from the European Bioinformatics Institute and Dr.  ... 
doi:10.1186/s13321-020-0408-x pmid:33430992 fatcat:bvdcvjhi4jhlnifpc25t6cjthq

Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones

Robert D. Clark, Denise N. Morris, Gary Chinigo, Michael S. Lawless, Jacques Prudhomme, Karine G. Le Roch, Maria José Lafuente, Santiago Ferrer, Francisco Javier Gamo, Robert Gadwood, Walter S. Woltosz
2020 Journal of Computer-Aided Molecular Design  
Their synthesis also represented an opportunity to prospectively validate our in silico property predictions.  ...  By applying a pair of complementary quantitative structure-activity relationships derived for inhibition of a truncated, soluble form of the enzyme from Plasmodium falciparum (s-PfDHODH) to data from a  ...  her careful reading of an earlier version of the manuscript and editorial suggestions.  ... 
doi:10.1007/s10822-020-00333-x pmid:32833084 fatcat:vsheydz4bjhvll2gfgzqq2t2eu
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