Computational and Structural Biotechnology Journal

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Computational and Structural Biotechnology Journal

Computational and Structural Biotechnology Journal (ISSN 2001-0370) is an online journal publishing research articles and reviews after full peer review.

Computational and Structural Biotechnology Journal (CSBJ) is an open access journal (Impact Factor 4.5) and is composed of four specialty sections:
• General • Smart Hospital • Nanoscience and Advanced Materials • Quantum Biology and Biophotonics. All articles are published, without barriers to access, immediately upon acceptance. The journal places a strong emphasis on functional and mechanistic

understanding of how molecular components in a biological process work together through the application of computational methods. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. Specific areas of interest include, but are not limited to:

• Structure and function of proteins, nucleic acids and other macromolecules
• Structure and function of multi-component complexes
• Protein folding, processing and degradation
• Enzymology
• Computational and structural studies of plant systems
• Microbial Informatics
• Genomics
• Proteomics
• Metabolomics
• Algorithms and Hypothesis in Bioinformatics
• Computational Chemistry & Drug Discovery
• Microscopy and Molecular Imaging
• Nanotechnology

While all general topics related to Computational and Structural Biology are welcomed, the editors reserve the right to pre-screen submissions based on the suitability of the topic of a submission and, therefore, the right as whether a manuscript will be processed/reviewed or not. Even though experimental validation is not required for publication, reliability and significance of biological discovery are validated and enriched by experimental studies. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and enables the rapid publication of papers under the following categories:

• Research articles
• Review articles
• Mini Reviews
• Highlights
• Communications
• Software/Web server articles
• Methods articles
• Database articles
• Book Reviews
• Meeting Reviews

12/10/2025

🧬 How does a foodborne toxin punch holes in our cells?

This study unveils the first comprehensive structural models of the Clostridium perfringens enterotoxin (CPE)–claudin complex — shedding light on how this foodborne pathogen forms lethal pores in intestinal cells and disrupts epithelial integrity.

By combining AlphaFold2 multimer predictions and molecular dynamics simulations, the researchers propose a detailed mechanism of pore assembly, cation selectivity, and membrane anchoring, advancing our molecular understanding of toxin-mediated cell damage.

📝 Santhosh Kumar Nagarajan, Joy Weber, Daniel Roderer, Jörg Piontek.

🔗 C. perfringens enterotoxin-claudin pore complex: Models for structure, mechanism of pore assembly and cation permeability. DOI: https://doi.org/10.1016/j.csbj.2024.11.048

📚 CSBJ: https://www.csbj.org/

Computational and Structural Biotechnology Journal

11/10/2025

🧬 Can quantum intelligence unlock new ways to understand genetic mutations?

This study introduces QuanGAT, a pioneering hybrid framework that merges Quantum Neural Networks (QNNs), Graph Attention Networks (GATs), and Federated Learning to predict DNA mutations — bridging quantum computing and biomedical AI in a privacy-preserving environment.

📝 Sotirios Messinis, Ioannis Rallis, Nikolaos Temenos, Dimitrios Kalogeras, George A. Kastis, Nikolaos Doulamis, Nicholas E. Protonotarios.

🔗 Quantum neural networks meet federated learning for DNA mutation prediction. DOI: https://doi.org/10.1016/j.csbj.2025.09.036

📚 CSBJ Quantum Biology & Biophotonics: https://www.csbj.org/qbio

Computational and Structural Biotechnology Journal

08/10/2025

🧬 Can controlling PARP1 turn CRISPR from a gene scissor into a gene sculptor?

This new study investigates how PARP1, a key DNA repair enzyme, influences the outcomes of CRISPR/Cas9-induced double-strand break (DSB) repair in proliferating cells. Using luminescent and fluorescent reporter assays, researchers reveal how PARP1 acts as a regulator that can shift the balance between error-prone and precise DNA repair.

📝 Tobias Wimmer, Judith Schneider, Fatimah Alabudeeb, Franziska M. Türk, Lyubomyr Lytvynchuk, Knut Stieger.

🔗 Influence of PARP1 on CRISPR/Cas9 induced double strand break repair in proliferating cells. DOI: https://doi.org/10.1016/j.csbj.2025.10.001

📚 CSBJ: https://www.csbj.org/

Computational and Structural Biotechnology Journal

07/10/2025

🧬 Where’s the tipping point between refinement and distortion in RNA molecular dynamics simulations?

This study provides the first systematic benchmark on when molecular dynamics (MD) actually improves RNA 3D structure models — offering data-driven insights and practical guidelines for the RNA modeling community. Using 61 RNA models from CASP15, the researchers reveal when MD refines, stabilizes, or deteriorates predicted RNA structures.

📝 Chandran Nithin, Smita P. Pilla, Sebastian Kmiecik.

🔗 When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines. DOI: https://doi.org/10.1016/j.csbj.2025.10.003

📚 CSBJ: https://www.csbj.org/

Computational and Structural Biotechnology Journal

07/10/2025

🤖🩺 Could transparency be the real prescription for ethical AI in healthcare?

This study introduces the AI Model Passport — a novel framework that ensures traceability, transparency, and accountability across the entire AI lifecycle in healthcare. Acting as a digital identity for AI models, it bridges the gap between documentation and regulation, empowering developers, clinicians, and regulators to build trustworthy, reproducible, and compliant AI systems.

📝 Varvara Kalokyri, Nikolaos S. Tachos, Charalampos N. Kalantzopoulos, Stelios Sfakianakis, Haridimos Kondylakis, Dimitrios I. Zaridis, Sara Colantonio, Daniele Regge, Nikolaos Papanikolaou, The ProCAncer-I consortium, Konstantinos Marias, Dimitrios I. Fotiadis, Manolis Tsiknakis.

🔗 AI Model Passport: Data and system traceability framework for transparent AI in health. DOI: https://doi.org/10.1016/j.csbj.2025.09.041

📚 CSBJ Smart Hospital: https://www.csbj.org/smarthospital

Computational and Structural Biotechnology Journal

03/10/2025

🧬 Can DNA molecules become the most reliable “hard drives” ever created?

This study introduces Pantheon-DNA, a versatile end-to-end system for DNA data storage that integrates encoding, decoding, and adaptive preprocessing algorithms – paving the way for scalable, high-fidelity, and cost-efficient molecular data storage.

📝 Adriano Galindo Leal, Thiago Yuji Aoyagi, André Guilherme Costa-Martins, Diego Trindade de Souza, Cristina Maria Ferreira da Silva, Eduardo Takeo Ueda, Marcelo Gonzaga de Oliveira Parada, Allan Eduardo Feitosa, André Fujita.

🔗 Pantheon-DNA: Versatile encoding-decoding system with integrated adaptive NGS preprocessing algorithms for DNA data storage. DOI: https://doi.org/10.1016/j.csbj.2025.09.002

📚 CSBJ: https://www.csbj.org/

Computational and Structural Biotechnology Journal

03/10/2025

🦠 What makes antimicrobial peptides so selective against bacteria and cancer cells, while leaving healthy cells intact?

This study unlocks the specificity of antimicrobial peptide (AMP) interactions with lipid membranes – paving the way for next-generation membrane-targeted therapies against infections, cancer, and even aging-related diseases. 🧬

Using molecular dynamics and metadynamics simulations, the authors provide a detailed framework for understanding how AMPs selectively bind to diseased cell membranes while sparing healthy ones.

📝 Daniel Conde-Torres, Martín Calvelo, Carme Rovira, Ángel Piñeiro, Rebeca Garcia-Fandino.

🔗 Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies. DOI: https://doi.org/10.1016/j.csbj.2024.04.022

📚 CSBJ Nanoscience & Advanced Materials: https://csbj.org/nano

Computational and Structural Biotechnology Journal

02/10/2025

🍽️🧠 What makes the ghrelin receptor so adaptable — controlling both hunger and memory at the molecular level?

This study takes an atomic-level look at the ghrelin receptor (GHSR) — a key G protein-coupled receptor (GPCR) known for regulating appetite and memory — and its dynamic interactions with different cellular partners (G proteins & arrestins). Using molecular dynamics simulations, the authors uncover how GHSR’s conformational shifts shape its signaling versatility.

📝 Carlos A.V. Barreto, Irina S. Moreira.

🔗 An atomic look at the interface of GHSR and its partners. DOI: https://doi.org/10.1016/j.csbj.2024.11.035

📚 CSBJ: https://www.csbj.org/

, Computational and Structural Biotechnology Journal

02/10/2025

💉 Could buffer design revolutionize how we detect circulating tumor cells (CTCs) in cancer patients?

This study introduces a novel buffer design for immunomagnetic-negative separation, significantly enhancing the enrichment of circulating tumor cells (CTCs) from patient blood samples — a breakthrough for liquid biopsy and cancer monitoring.

📝 Kazuaki Hoshi, Yasinjan Hashim, Shinsaku Togo, Shoko Saiwaki, Hiroaki Motomura, Issei Sumiyoshi, Shun Nakazawa, Yusuke Ochi, Chieko Miyoshi, Rihyang Heo, Yoko Tabe, Kanae Abe, Yasuo Urata, Kazuhisa Takahashi.

🔗 Design of buffer property for the new enrichment method of circulating tumor cell based on immunomagnetic-negative separation. DOI: https://doi.org/10.1016/j.csbj.2024.11.033

📚 CSBJ Nanoscience & Advanced Materials: https://csbj.org/nano

, Computational and Structural Biotechnology Journal

01/10/2025

🧬 Is a “common deletion” in mitochondrial DNA the hidden link between energy metabolism and cancer?

This review explores the mitochondrial DNA common deletion (mtDNA-CD) — a 4,977 bp mutation long studied for its potential role in cancer. Despite decades of research, its exact impact remains unclear, but new evidence and advanced methods are opening the door to answers.

📝 Mun Kay Ho, Joshua W.K. Ho.

🔗 Mitochondrial DNA common deletion in cancer: Emerging evidence and methodological challenges. DOI: https://doi.org/10.1016/j.csbj.2025.09.010

📚 CSBJ: https://www.csbj.org/

, Computational and Structural Biotechnology Journal

01/10/2025

🧠 Could at-home brain monitoring be the future of migraine management?

This study explores how telemedicine and telemonitoring tools—an E-diary app and a home-based EEG system—are enhancing personalized migraine care and advancing research. By bringing monitoring into patients’ homes, these solutions offer a scalable, user-friendly way to manage migraine more effectively.

📝 A.S.J.C. Oosterlee, B.W.H. van der Arend, J.L. Duijvelshoff, M. van de Ruit, G.M. Terwindt

🔗 Enhancing migraine care and research through Telemedicine and telemonitoring: E-diary tracking and home EEG. https://doi.org/10.1016/j.csbj.2025.09.007

📚 CSBJ Smart Hospital: https://www.csbj.org/smarthospital

, Computational and Structural Biotechnology Journal

30/09/2025

🧠 Could reprogramming RNA offer a new path to brain aneurysm therapies?

This study explores the RNA editing landscape in intracranial aneurysms (IA) and uncovers how post-transcriptional mechanisms like RNA editing (RE) and alternative splicing (AS) may drive aneurysm rupture — offering fresh insights into diagnosis and treatment strategies.

📝 Yulan Wang, Qingqing Li, Peipei Wang, Tianyi Xu, Xintong Zhao, Mingquan Ye.

🔗 In-depth analysis of the RNA editing landscape in intracranial aneurysms and its potential role in alternative splicing. DOI: https://doi.org/10.1016/j.csbj.2025.09.021

📚 CSBJ: https://www.csbj.org/

, Computational and Structural Biotechnology Journal

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