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AI Driven Structural and Functional Genomics and Translational Medicine

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 3332

Special Issue Editor


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Guest Editor
Georgia Institute of Technology, Atlanta, GA 30332, USA
Interests: protein chemistry; structural biology; crystallography; drug discovery

Special Issue Information

Dear Colleagues,

With the advancement of AI and machine learning methods in the recent years, computational biology has not only led to breakthroughs in fundamental science and technology, but also made significant positive impacts on human health and environmental sustainability. For example, in 2020, Alpha-Fold has set a new benchmark of improved accuracy on protein structure predictions which serves the basis for many useful applications, including disease mutation 3D structural mapping and accelerated drug discovery. At the molecular level, computational biology enables increasingly accurate predictions of structure and functions of macromolecular biomolecules and their interactions with each other and small molecules. On the genomic and system biology scale, AI and machine learning methods have demonstrated their roles in interdisciplinary research involving the “Design–Build–Test–Learn“ (DBTL) cycle and accelerated biomedical research in all stages from in silico and bench to bedside and ultimately improved the quality of our daily life. We would like to take this opportunity to invite submissions of new cutting-edge research in the areas of computational biology with a focus on new methods in structural and functional predictions of proteome, genetics and epigenetics, drug discovery, virtual screening, and translational medicine.

Dr. Hongnan Cao
Guest Editor

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Keywords

  • computational method
  • protein chemistry
  • structure and functions
  • drug discovery
  • virtual screening

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Published Papers (1 paper)

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Research

19 pages, 3703 KiB  
Article
Adera2.0: A Drug Repurposing Workflow for Neuroimmunological Investigations Using Neural Networks
by Marzena Lazarczyk, Kamila Duda, Michel Edwar Mickael, Onurhan AK, Justyna Paszkiewicz, Agnieszka Kowalczyk, Jarosław Olav Horbańczuk and Mariusz Sacharczuk
Molecules 2022, 27(19), 6453; https://doi.org/10.3390/molecules27196453 - 30 Sep 2022
Cited by 5 | Viewed by 2844
Abstract
Drug repurposing in the context of neuroimmunological (NI) investigations is still in its primary stages. Drug repurposing is an important method that bypasses lengthy drug discovery procedures and focuses on discovering new usages for known medications. Neuroimmunological diseases, such as Alzheimer’s, Parkinson’s, multiple [...] Read more.
Drug repurposing in the context of neuroimmunological (NI) investigations is still in its primary stages. Drug repurposing is an important method that bypasses lengthy drug discovery procedures and focuses on discovering new usages for known medications. Neuroimmunological diseases, such as Alzheimer’s, Parkinson’s, multiple sclerosis, and depression, include various pathologies that result from the interaction between the central nervous system and the immune system. However, the repurposing of NI medications is hindered by the vast amount of information that needs mining. We previously presented Adera1.0, which was capable of text mining PubMed for answering query-based questions. However, Adera1.0 was not able to automatically identify chemical compounds within relevant sentences. To challenge the need for repurposing known medications for neuroimmunological diseases, we built a deep neural network named Adera2.0 to perform drug repurposing. The workflow uses three deep learning networks. The first network is an encoder and its main task is to embed text into matrices. The second network uses a mean squared error (MSE) loss function to predict answers in the form of embedded matrices. The third network, which constitutes the main novelty in our updated workflow, also uses a MSE loss function. Its main usage is to extract compound names from relevant sentences resulting from the previous network. To optimize the network function, we compared eight different designs. We found that a deep neural network consisting of an RNN neural network and a leaky ReLU could achieve 0.0001 loss and 67% sensitivity. Additionally, we validated Adera2.0’s ability to predict NI drug usage against the DRUG Repurposing Hub database. These results establish the ability of Adera2.0 to repurpose drug candidates that can shorten the development of the drug cycle. The workflow could be download online. Full article
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