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Chapter
Mold2 Descriptors Facilitate Development of Machine Learning and Deep Learning Models for Predicting Toxicity of Chemicals
Numerical description of chemical structures is necessary for development of machine learning and deep learning models for predicting the potential toxicity of chemicals. Mold2 is a software tool developed in ...
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Protocol
Machine Learning Models for Predicting Liver Toxicity
Liver toxicity is a major adverse drug reaction that accounts for drug failure in clinical trials and withdrawal from the market. Therefore, predicting potential liver toxicity at an early stage in drug discov...
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Article
Open AccessInforming selection of drugs for COVID-19 treatment through adverse events analysis
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic and there is an urgent need for safe and effective drugs for COVID-19 treatment. Since develo** a new drug is time consuming, many approved or inves...
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Article
Open AccessCorrection to: Similarities and differences between variants called with human reference genome HG19 or HG38
After publication of this supplement article
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Article
Open AccessSimilarities and differences between variants called with human reference genome HG19 or HG38
Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38....
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Chapter
Applications of Molecular Dynamics Simulations in Computational Toxicology
is a discipline seeking to computationally and predict toxicity of chemicals including drugs, food additives, and other . of chemicals using current or is at best time-consuming and expensive. ...
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Article
Open AccesssNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides
Understanding the binding between human leukocyte antigens (HLAs) and peptides is important to understand the functioning of the immune system. Since it is time-consuming and costly to measure the binding betw...
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Article
Theoretical approaches to identify the potent scaffold for human sirtuin1 activator: Bayesian modeling and density functional theory
Bayesian and pharmacophore modeling approaches were utilized to identify the fragments and critical chemical features of small molecules that enhance sirtuin1 (SIRT1) activity. Initially, 48 Bayesian models (B...
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Article
Discovery of potent inhibitors for interleukin-2-inducible T-cell kinase: structure-based virtual screening and molecular dynamics simulation approaches
In our study, a structure-based virtual screening study was conducted to identify potent ITK inhibitors, as ITK is considered to play an important role in the treatment of inflammatory diseases. We developed a...
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Article
Combined chemical feature-based assessment and Bayesian model studies to identify potential inhibitors for Factor Xa
In our study, we have described chemical feature-based 3D QSAR pharmacophore models with help of known inhibitors of Factor Xa (FXa). The best model, Hypo1, has validated by various techniques to prove its rob...
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Article
Pharmacophore modeling, molecular docking, and molecular dynamics simulation approaches for identifying new lead compounds for inhibiting aldose reductase 2
Aldose reductase 2 (ALR2), which catalyzes the reduction of glucose to sorbitol using NADP as a cofactor, has been implicated in the etiology of secondary complications of diabetes. A pharmacophore model, Hypo...
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Article
Pharmacophore-based virtual screening and density functional theory approach to identifying novel butyrylcholinesterase inhibitors
To identify the critical chemical features, with reliable geometric constraints, that contributes to the inhibition of butyrylcholinesterase (BChE) function.
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Article
Homology modeling, molecular dynamics, e-pharmacophore map** and docking study of Chikungunya virus nsP2 protease
To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. ...
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Article
Open AccessPotent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies
Beta-site amyloid precursor protein cleaving enzyme (BACE-1) is a single-membrane protein belongs to the aspartyl protease class of catabolic enzymes. This enzyme involved in the processing of the amyloid prec...
