Advances in Structural Bioinformatics and Next-Generation Sequence Analysis for Drug Design

A special issue of BioMedInformatics (ISSN 2673-7426).

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4858

Special Issue Editor


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Guest Editor
Department of Biological Research on the Red Blood Cells, INTS, INSERM UMR_S 1134, Université de Paris, Université de la Réunion, 75739 Paris, France
Interests: structural bioinformatics; bioinformatics; next-generation sequence; drug design; deep learning
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Special Issue Information

Dear Colleagues,

Structural Bioinformatics and Next-Generation Sequencing (NGS) are two emerging fields that have revolutionized the way we approach drug design. Structural Bioinformatics allows us to analyze the three-dimensional structures of proteins and other biological macromolecules and to gain insights into their functions and interactions. NGS has enabled us to sequence large amounts of genetic data quickly and efficiently and to explore the genetic basis of diseases and drug responses.

This Special Issue aims to bring together researchers and practitioners working in the areas of Structural Bioinformatics, Bioinformatics, Next-Generation Sequencing, Drug Design, and Deep Learning. We welcome original research articles that report on novel and significant findings in these areas.

Scope and Topics:

We invite high-quality research papers that report on innovative and significant research findings in the following areas:

    Structural Bioinformatics for Drug Design
    Computational methods for analyzing protein–ligand interactions;
    Next-Generation Sequencing for Personalized Medicine;
    Genomic data analysis for drug discovery;
    Deep learning in structural biology and drug design;

Submission Guidelines:

We welcome original and unpublished research articles that report on innovative and significant research findings in the field of Structural Bioinformatics and Next-Generation Sequencing for Drug Design. The submissions should not have been published elsewhere and should not be under consideration for publication in any other venue. We only accept full-length research articles for this Special Issue, and we encourage authors to follow the standard research paper format and provide a clear and concise description of their research findings.

All submitted papers will be peer-reviewed by experts in the field. Manuscripts should be submitted in English, and the submission should adhere to the journal's guidelines and formatting requirements.

Conclusion:

This Special Issue aims to present cutting-edge research in the field of Structural Bioinformatics and Next-Generation Sequencing for Drug Design. We welcome high-quality research papers that report on novel and significant research findings in these areas. We look forward to receiving your submissions and making this Special Issue a success.

Prof. Dr. Alexandre G. De Brevern
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. BioMedInformatics is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • structural Bioinformatics for drug design
  • computational methods for analyzing protein–ligand interactions
  • next-generation sequencing for personalized medicine
  • genomic data analysis for drug discovery
  • deep learning in structural biology and drug design

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Published Papers (3 papers)

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Review

21 pages, 831 KiB  
Review
Computational Strategies to Enhance Cell-Free Protein Synthesis Efficiency
by Iyappan Kathirvel and Neela Gayathri Ganesan
BioMedInformatics 2024, 4(3), 2022-2042; https://doi.org/10.3390/biomedinformatics4030110 - 10 Sep 2024
Viewed by 595
Abstract
Cell-free protein synthesis (CFPS) has emerged as a powerful tool for protein production, with applications ranging from basic research to biotechnology and pharmaceutical development. However, enhancing the efficiency of CFPS systems remains a crucial challenge for realizing their full potential. Computational strategies offer [...] Read more.
Cell-free protein synthesis (CFPS) has emerged as a powerful tool for protein production, with applications ranging from basic research to biotechnology and pharmaceutical development. However, enhancing the efficiency of CFPS systems remains a crucial challenge for realizing their full potential. Computational strategies offer promising avenues for optimizing CFPS efficiency by providing insights into complex biological processes and enabling rational design approaches. This review provides a comprehensive overview of the computational approaches aimed at enhancing CFPS efficiency. The introduction outlines the significance of CFPS and the role of computational methods in addressing efficiency limitations. It discusses mathematical modeling and simulation-based approaches for predicting protein synthesis kinetics and optimizing CFPS reactions. The review also delves into the design of DNA templates, including codon optimization strategies and mRNA secondary structure prediction tools, to improve protein synthesis efficiency. Furthermore, it explores computational techniques for engineering cell-free transcription and translation machinery, such as the rational design of expression systems and the predictive modeling of ribosome dynamics. The predictive modeling of metabolic pathways and the energy utilization in CFPS systems is also discussed, highlighting metabolic flux analysis and resource allocation strategies. Machine learning and artificial intelligence approaches are being increasingly employed for CFPS optimization, including neural network models, deep learning algorithms, and reinforcement learning for adaptive control. This review presents case studies showcasing successful CFPS optimization using computational methods and discusses applications in synthetic biology, biotechnology, and pharmaceuticals. The challenges and limitations of current computational approaches are addressed, along with future perspectives and emerging trends, such as the integration of multi-omics data and advances in high-throughput screening. The conclusion summarizes key findings, discusses implications for future research directions and applications, and emphasizes opportunities for interdisciplinary collaboration. This review offers valuable insights and prospects regarding computational strategies to enhance CFPS efficiency. It serves as a comprehensive resource, consolidating current knowledge in the field and guiding further advancements. Full article
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16 pages, 1545 KiB  
Review
Unlocking the Future of Drug Development: Generative AI, Digital Twins, and Beyond
by Zamara Mariam, Sarfaraz K. Niazi and Matthias Magoola
BioMedInformatics 2024, 4(2), 1441-1456; https://doi.org/10.3390/biomedinformatics4020079 - 6 Jun 2024
Cited by 1 | Viewed by 1354
Abstract
This article delves into the intersection of generative AI and digital twins within drug discovery, exploring their synergistic potential to revolutionize pharmaceutical research and development. Through various instances and examples, we illuminate how generative AI algorithms, capable of simulating vast chemical spaces and [...] Read more.
This article delves into the intersection of generative AI and digital twins within drug discovery, exploring their synergistic potential to revolutionize pharmaceutical research and development. Through various instances and examples, we illuminate how generative AI algorithms, capable of simulating vast chemical spaces and predicting molecular properties, are increasingly integrated with digital twins of biological systems to expedite drug discovery. By harnessing the power of computational models and machine learning, researchers can design novel compounds tailored to specific targets, optimize drug candidates, and simulate their behavior within virtual biological environments. This paradigm shift offers unprecedented opportunities for accelerating drug development, reducing costs, and, ultimately, improving patient outcomes. As we navigate this rapidly evolving landscape, collaboration between interdisciplinary teams and continued innovation will be paramount in realizing the promise of generative AI and digital twins in advancing drug discovery. Full article
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19 pages, 2539 KiB  
Review
Transforming Drug Design: Innovations in Computer-Aided Discovery for Biosimilar Agents
by Shadi Askari, Alireza Ghofrani and Hamed Taherdoost
BioMedInformatics 2023, 3(4), 1178-1196; https://doi.org/10.3390/biomedinformatics3040070 - 8 Dec 2023
Cited by 4 | Viewed by 1986
Abstract
In pharmaceutical research and development, pursuing novel therapeutics and optimizing existing drugs have been revolutionized by the fusion of cutting-edge technologies and computational methodologies. Over the past few decades, the field of drug design has undergone a remarkable transformation, catalyzed by the rapid [...] Read more.
In pharmaceutical research and development, pursuing novel therapeutics and optimizing existing drugs have been revolutionized by the fusion of cutting-edge technologies and computational methodologies. Over the past few decades, the field of drug design has undergone a remarkable transformation, catalyzed by the rapid advancement of computer-aided discovery techniques and the emergence of biosimilar agents. This dynamic interplay between scientific innovation and technological prowess has expedited the drug discovery process and paved the way for more targeted, effective, and personalized treatment approaches. This review investigates the transformative computer-aided discovery techniques for biosimilar agents in reshaping drug design. It examines how computational methods expedite drug candidate identification and explores the rise of cost-effective biosimilars as alternatives to biologics. Through this analysis, this study highlights the potential of these innovations to enhance the efficiency and accessibility of pharmaceutical development. It represents a pioneering effort to examine how computer-aided discovery is revolutionizing biosimilar agent development, exploring its applications, challenges, and prospects. Full article
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