Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness
Potts Hamiltonian models of protein sequence co-variation are statistical models constructed
from the pair correlations observed in a multiple sequence alignment (MSA) of a protein …
from the pair correlations observed in a multiple sequence alignment (MSA) of a protein …
Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants
HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is
mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors …
mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors …
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies
RHY Louie, KJ Kaczorowski… - Proceedings of the …, 2018 - National Acad Sciences
HIV is a highly mutable virus, and over 30 years after its discovery, a vaccine or cure is still
not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected …
not available. The isolation of broadly neutralizing antibodies (bnAbs) from HIV-infected …
A perspective on the role of computational models in immunology
AK Chakraborty - Annual review of immunology, 2017 - annualreviews.org
This is an exciting time for immunology because the future promises to be replete with
exciting new discoveries that can be translated to improve health and treat disease in novel …
exciting new discoveries that can be translated to improve health and treat disease in novel …
100th anniversary of macromolecular science viewpoint: data-driven protein design
The design of synthetic proteins with the desired function is a long-standing goal in
biomolecular science, with broad applications in biochemical engineering, agriculture …
biomolecular science, with broad applications in biochemical engineering, agriculture …
Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis
Direct-acting antiviral agents (DAAs) provide efficacious therapeutic treatments for chronic
Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) …
Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) …
Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape
Vaccination has essentially eradicated poliovirus. Yet, its mutation rate is higher than that of
viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness …
viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness …
Epistasis and entrenchment of drug resistance in HIV-1 subtype B
The development of drug resistance in HIV is the result of primary mutations whose effects
on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis' …
on viral fitness depend on the entire genetic background, a phenomenon called 'epistasis' …
Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease
Understanding the complex mutation patterns that give rise to drug resistant viral strains
provides a foundation for develo** more effective treatment strategies for HIV/AIDS …
provides a foundation for develo** more effective treatment strategies for HIV/AIDS …
Epistatic contributions promote the unification of incompatible models of neutral molecular evolution
JA de la Paz, CM Nartey, M Yuvaraj… - Proceedings of the …, 2020 - National Acad Sciences
We introduce a model of amino acid sequence evolution that accounts for the statistical
behavior of real sequences induced by epistatic interactions. We base the model dynamics …
behavior of real sequences induced by epistatic interactions. We base the model dynamics …