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HIV-1

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Characterization of low level viraemia in HIV-infected patients receiving boosted protease inhibitor-based antiretroviral regimens.

HIV research & clinical practice
To understand the pathogenesis of low level viraemia (LLV) in HIV-infected patients on boosted protease inhibitors (PI/b), we enrolled 34 subjects with a median HIV-RNA 79 copies/mL and followed them for 15 months. Samples for next generation sequenc...

A Ligand-Based Virtual Screening Method Using Direct Quantification of Generalization Ability.

Molecules (Basel, Switzerland)
Machine learning plays an important role in ligand-based virtual screening. However, conventional machine learning approaches tend to be inefficient when dealing with such problems where the data are imbalanced and features describing the chemical ch...

Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method.

International journal of molecular sciences
Human immunodeficiency virus type-1 and hepatitis C virus (HIV/HCV) coinfection occurs when a patient is simultaneously infected with both human immunodeficiency virus type-1 (HIV-1) and hepatitis C virus (HCV), which is common today in certain popul...

Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints.

Journal of chemical information and modeling
Discovery and optimization of small molecule inhibitors as therapeutic drugs have immensely benefited from rational structure-based drug design. With recent advances in high-resolution structure determination, computational power, and machine learnin...

Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates.

Scientific reports
Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have promising utility in prevention and treatment of HIV-1 infection, and several are currently undergoing clinical trials. Due to the high sequence diversity an...

Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Journal of chemical theory and computation
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few clo...

Super learner analysis of real-time electronically monitored adherence to antiretroviral therapy under constrained optimization and comparison to non-differentiated care approaches for persons living with HIV in rural Uganda.

Journal of the International AIDS Society
INTRODUCTION: Real-time electronic adherence monitoring (EAM) systems could inform on-going risk assessment for HIV viraemia and be used to personalize viral load testing schedules. We evaluated the potential of real-time EAM (transferred via cellula...

Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data.

Viruses
The fast replication rate and lack of repair mechanisms of human immunodeficiency virus (HIV) contribute to its high mutation frequency, with some mutations resulting in the evolution of resistance to antiretroviral therapies (ART). As such, studying...

Evolution of drug resistance in HIV protease.

BMC bioinformatics
BACKGROUND: Drug resistance is a critical problem limiting effective antiviral therapy for HIV/AIDS. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of therapy. These techniques...