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New Computational Methodologies for Biomolecule Sequence, Structure and Function Discovery: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 749

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School of Computer Science and Engineering, Central South University, Changsha 410083, China
Interests: machine learning; deep learning; data mining; bioinformatics
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Special Issue Information

Dear Colleagues,

With the accumulation of large-scale data in bioinformatics, researchers deal with several types of biomolecule data, such as sequences, structures, and functions. The question of how to effectively use these data in the fields of biology is an important one, as many researchers apply computational methods to analyze enzymes, identify biomolecules and biological networks, study structural proteomics, analyze gene expression, perform molecular docking, assess post-translational modifications, and more. Many new computational methodologies have been developed for biomolecule sequence, structure, and function discovery. The novel methods presented in these studies propose new tools for tackling different problems in bioinformatics, and the new findings therein promise to provide new insights for biologists and medical scientists.

This Special Issue focuses on studies introducing novel computational methodologies and high-quality benchmark datasets for the discovery of biomolecule sequences, structures, and functions. Thus, we welcome original research articles, reviews, and communications covering one or more of the following topics:

  • Bioinformatics;
  • Machine learning;
  • Deep learning;
  • Biomolecule identification;
  • Biological networks;
  • Structural proteomics;
  • Gene expression analysis;
  • Molecular docking;
  • Post-translational modifications.

Prof. Dr. Fei Guo
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • bioinformatics
  • machine learning
  • deep learning
  • biomolecule identification
  • biological networks
  • structural proteomics
  • gene expression analysis
  • molecular docking
  • post-translational modifications

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Published Papers (1 paper)

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Research

27 pages, 1134 KB  
Article
TC-HUR: A Tri-Phase Cauchy-Assisted Hunger Games Search and Unified Runge–Kutta Optimizer for Robust DNA Data Storage
by Beyza Öztürk, Ayşenur İgit, Aylin Kaya, Zeynep Tuğsem Çamlıca, Selen Arıcı and Muhammed Faruk Şahin
Int. J. Mol. Sci. 2026, 27(7), 3134; https://doi.org/10.3390/ijms27073134 - 30 Mar 2026
Viewed by 511
Abstract
Although DNA-based data storage theoretically provides an information density of 2 bits per nucleotide, biochemical constraints transform sequence design into a high-dimensional constrained combinatorial optimization problem. The high computational cost and low encoding efficiency of conventional rule-based approaches make metaheuristic methods an effective [...] Read more.
Although DNA-based data storage theoretically provides an information density of 2 bits per nucleotide, biochemical constraints transform sequence design into a high-dimensional constrained combinatorial optimization problem. The high computational cost and low encoding efficiency of conventional rule-based approaches make metaheuristic methods an effective alternative. This study proposes the TC-HUR hybrid algorithm to simultaneously optimize information density and conflicting biophysical constraints, including homopolymer (HP) length, GC content, melting temperature (Tm), and reverse-complement (RC) similarity. The method escapes local optima using Cauchy jump-enhanced Hunger Games Search (HGS), performs high-precision exploitation via Runge–Kutta (RUN) operators, and refines constraint violations at the nucleotide level through an adaptive intensive mutation mechanism. The algorithm is evaluated on a complex dataset of 1853 nucleotides under different noise regimes. TC-HUR outperforms RUN by 2.5% and HGS by 16.7% in average fitness. While maintaining homopolymer length near the ideal threshold, it reduces reverse-complement similarity to 19.10%, ensuring high sequence diversity. Under high-noise conditions, TC-HUR achieves a normalized edit distance of 0.1290, reducing insertion–deletion (indel) errors by approximately 14%. The results demonstrate that the proposed model effectively generates biophysically synthesizable and noise-resilient DNA codes. Full article
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