A Case-Based Reasoning System for Genotypic Prediction of Hiv-1 Co-Receptor Tropism

Evans, Mark C.; Paquet, Agnès; Huang, Wei; Napolitano, Laura A.; Frantzell, Arne; Toma, Jonathan; Stawiski, Eric; Goetz, Matthew Bidwell; Petropoulos, Christos J.; Whitcomb, Jeannette M.; Coakley, Eoin; Haddad, Mojgan

doi:10.1142/s0219720013500066

Cited by 3 publications

(2 citation statements)

References 30 publications

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“…These have also been reported previously for prediction of other important peptides viz., ABCpred, AntiCP, QSPpred, and so forth. Evans et al have also described HIV coreceptor tropism prediction on the basis of the amino‐acid sites and physiochemical characteristics of the V3 loop sequence of the HIV envelope.…”

Section: Discussionmentioning

confidence: 99%

AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)

2015

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Peptide-based antiviral therapeutics has gradually paved their way into mainstream drug discovery research. Experimental determination of peptides' antiviral activity as expressed by their IC50 values involves a lot of effort. Therefore, we have developed "AVP-IC50 Pred," a regression-based algorithm to predict the antiviral activity in terms of IC50 values (μM). A total of 759 non-redundant peptides from AVPdb and HIPdb were divided into a training/test set having 683 peptides (T(683)) and a validation set with 76 independent peptides (V(76)) for evaluation. We utilized important peptide sequence features like amino-acid compositions, binary profile of N8-C8 residues, physicochemical properties and their hybrids. Four different machine learning techniques (MLTs) namely Support vector machine, Random Forest, Instance-based classifier, and K-Star were employed. During 10-fold cross validation, we achieved maximum Pearson correlation coefficients (PCCs) of 0.66, 0.64, 0.56, 0.55, respectively, for the above MLTs using the best combination of feature sets. All the predictive models also performed well on the independent validation dataset and achieved maximum PCCs of 0.74, 0.68, 0.59, 0.57, respectively, on the best combination of feature sets. The AVP-IC50 Pred web server is anticipated to assist the researchers working on antiviral therapeutics by enabling them to computationally screen many compounds and focus experimental validation on the most promising set of peptides, thus reducing cost and time efforts. The server is available at http://crdd.osdd.net/servers/ic50avp.

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Section: Discussionmentioning

confidence: 99%

AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)

2015

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“…Most of CBR systems collect data and run in specific domain only ( 8 , 14 - 16 ), but suggested Fuzzy CBR runs on the Android platform for mobile devices. Previous CBR systems used limited number of cases in their case base ( 2 , 3 , 5 , 17 , 18 ) while present Fuzzy CBR uses real online cases.…”

Section: Discussionmentioning

confidence: 99%

Designing and Implementation of Fuzzy Case-based Reasoning System on Android Platform Using Electronic Discharge Summary of Patients with Chronic Kidney Diseases

et al. 2016

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Introduction: Case-based reasoning (CBR) systems are one of the effective methods to find the nearest solution to the current problems. These systems are used in various spheres as well as industry, business, and economy. The medical field is not an exception in this regard, and these systems are nowadays used in the various aspects of diagnosis and treatment. Methodology: In this study, the effective parameters were first extracted from the structured discharge summary prepared for patients with chronic kidney diseases based on data mining method. Then, through holding a meeting with experts in nephrology and using data mining methods, the weights of the parameters were extracted. Finally, fuzzy system has been employed in order to compare the similarities of current case and previous cases, and the system was implemented on the Android platform. Discussion: The data on electronic discharge records of patients with chronic kidney diseases were entered into the system. The measure of similarity was assessed using the algorithm provided in the system, and then compared with other known methods in CBR systems. Conclusion: Developing Clinical fuzzy CBR system used in Knowledge management framework for registering specific therapeutic methods , Knowledge sharing environment for experts in a specific domain and Powerful tools at the point of care .

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Machine Learning in Discovery of New Antivirals and Optimization of Viral Infections Therapy

Tarasova

Poroikov

2021

CMC

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: Nowadays, computational approaches play an important role in the design of new drug-like compounds and optimization of pharmacotherapeutic treatment of diseases. The emerging growth of viral infections, including those caused by the Human Immunodeficiency Virus (HIV), Ebola virus, recently detected coronavirus, and some others, leads to many newly infected people with a high risk of death or severe complications. A huge amount of chemical, biological, clinical data is at the disposal of the researchers. Therefore, there are many opportunities to find the relationships between the particular features of chemical data and the antiviral activity of biologically active compounds based on machine learning approaches. Biological and clinical data can also be used for building models to predict relationships between viral genotype and drug resistance, which might help determine the clinical outcome of treatment. In the current study, we consider machine-learning approaches in the antiviral research carried out during the past decade. We overview in detail the application of machine-learning methods for the design of new potential antiviral agents and vaccines, drug resistance prediction, and analysis of virus-host interactions. Our review also covers the perspectives of using the machine-learning approaches for antiviral research, including Dengue, Ebola viruses, Influenza A, Human Immunodeficiency Virus, coronaviruses, and some others. Nowadays, computational approaches play an important role in the design of new drug-like compounds and optimization of pharmacotherapeutic treatment of diseases. The emerging growth of viral infections, including those caused by the Human Immunodeficiency Virus (HIV), Ebola virus, recently detected coronavirus, and some others, leads to many newly infected people with a high risk of death or severe complications. A huge amount of chemical, biological, clinical data is at the disposal of the researchers. Therefore, there are many opportunities to find the relationships between the particular features of chemical data and the antiviral activity of biologically active compounds based on machine learning approaches. Biological and clinical data can also be used for building models to predict relationships between viral genotype and drug resistance, which might help determine the clinical outcome of treatment. In the current study, we consider machine-learning approaches in the antiviral research carried out during the past decade. We overview in detail the application of machine-learning methods for the design of new potential antiviral agents and vaccines, drug resistance prediction, and analysis of virus-host interactions. Our review also covers the perspectives of using the machine-learning approaches for antiviral research, including Dengue, Ebola viruses, Influenza A, Human Immunodeficiency Virus, coronaviruses, and some others.

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A Case-Based Reasoning System for Genotypic Prediction of Hiv-1 Co-Receptor Tropism

Cited by 3 publications

References 30 publications

AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)

AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)

Designing and Implementation of Fuzzy Case-based Reasoning System on Android Platform Using Electronic Discharge Summary of Patients with Chronic Kidney Diseases

Machine Learning in Discovery of New Antivirals and Optimization of Viral Infections Therapy

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A Case-Based Reasoning System for Genotypic Prediction of Hiv-1 Co-Receptor Tropism

Cited by 3 publications

References 30 publications

AVP‐IC50Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50)

AVP‐IC50Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50)

Designing and Implementation of Fuzzy Case-based Reasoning System on Android Platform Using Electronic Discharge Summary of Patients with Chronic Kidney Diseases

Machine Learning in Discovery of New Antivirals and Optimization of Viral Infections Therapy

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AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)

AVP‐IC₅₀Pred: Multiple machine learning techniques‐based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC₅₀)