Detection of HIV-1 protease cleavages sites via hidden Markov model and physicochemical properties of aminoacids

Doğan Dar, Elif
Purutçuoğlu Gazi, Vilda
The detection of the cleavage side in Chip-seq data is one of the main interests to find the lock-and-key relationship between enzymes and prohibits in certain diseases such as AIDS and to produce the proper inhibitors for these illnesses. For this detection, different approaches like support vector machines and artificial neural networks have been suggested. In this study, we use the hidden Markov model (HMM) for the cleavage site detection. In our application, initially, we comprehensively explain the mathematical details of HMM and the inference of the model parameters, and then we discuss the effect of various clustering approaches both in feature selection and state formation. We demonstrate the calculation of each step in a toy and benchmark dataset and evaluate the accuracy of estimates with other approaches in the literature.


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Intravenous Immunoglobulin (IVIg) is mainly composed of IgG derived from pooled plasma of healthy individuals and used to treat variety of immune diseases. Low dose administration can activate the immune system in case of immunodeficiencies, while high doses suppress immune responses in autoimmune/autoinflammatory conditions. The mechanisms underlying this disparate effect is poorly understood. Herein, we examined the effects of IVIg treatment on the functionality of specific innate immune cell populations ...
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The Caco-2 colorectal cancer cell line is widely used as a model for intestinal differentiation and barrier function. These cells, upon reaching confluency, spontaneously differentiate into enterocyte-like cells, synthesize intestinal enzymes, and form domes. Caco-2 cells also undergo autophagy in the course of differentiation. The criteria to establish the induction of autophagy in cells are already well established. Here, we describe the protocol for the spontaneous differentiation of Caco-2 cells and the...
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AKR1B1 and AKR1B10, members of the aldo-keto reductase family of enzymes that participate in the polyol pathway of aldehyde metabolism, are aberrantly expressed in colon cancer. We previously showed that high expression of AKR1B1 (AKR1B1(HIGH)) was associated with enhanced motility, inflammation and poor clinical outcome in colon cancer patients. Using publicly available datasets and ex vivo gene expression analysis (n = 51, Ankara cohort), we have validated our previous in silico finding that AKR1B1(HIGH) ...
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Citation Formats
E. Doğan Dar and V. Purutçuoğlu Gazi, Detection of HIV-1 protease cleavages sites via hidden Markov model and physicochemical properties of aminoacids. 2020, p. 193.