ArticleProceedings of the National Academy of Sciences of the United States of America2010
Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Theoretical study of KRAS G12C secondary mutations influencing inhibitor resistance.Biophysics and physicobiology · 2026Article
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- The evolution of the HIV-1 protease folding stability.Virus evolution · 2022Article
- MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.Nucleic acids research · 2021Article
- A combined computational and experimental strategy identifies mutations conferring resistance to drugs targeting the BCR-ABL fusion protein.Communications biology · 2020Article
- Genome-wide association and epistatic interactions of flowering time in soybean cultivar.PloS one · 2020Article
- The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction.Structural dynamics (Melville, N.Y.) · 2018Article
- Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene-gene interactions.Scientific reports · 2017Article
- Observational
- A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies.BMC genomics · 2015Article
- Estimating HIV-1 fitness characteristics from cross-sectional genotype data.PLoS computational biology · 2014Article
- IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.PLoS computational biology · 2014Article
- P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape.PLoS computational biology · 2014Article
- Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis.BMC bioinformatics · 2014Article
- Identification of the critical sites of NNRTI-resistance in reverse transcriptase of HIV-1 CRF_BC strains.PloS one · 2014Article
- Article
- Article
- Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage.Bioinformatics (Oxford, England) · 2013Article
- Structure-based methods for predicting target mutation-induced drug resistance and rational drug design to overcome the problem.Drug discovery today · 2012Review
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Authors and funding
4 authors.
Funding
Abstract
We propose a systematic approach for a better understanding of how HIV viruses employ various combinations of mutations to resist drug treatments, which is critical to developing new drugs and optimizing the use of existing drugs. By probabilistically modeling mutations in the HIV-1 protease or reverse transcriptase (RT) isolated from drug-treated patients, we present a statistical procedure that first detects mutation combinations associated with drug resistance and then infers detailed interaction structures of these mutations. The molecular basis of our statistical predictions is further studied by using molecular dynamics simulations and free energy calculations. We have demonstrated the usefulness of this systematic procedure on three HIV drugs, (Indinavir, Zidovudine, and Nevirapine), discovered unique interaction features between viral mutations induced by these drugs, and revealed the structural basis of such interactions.
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