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25th Anniversary of IJMS: Updates and Advances in Molecular Informatics

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 December 2025 | Viewed by 258

Special Issue Editors


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Guest Editor
LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
Interests: theoretical and computational chemistry; electronic structure theory; quantum theory of atoms in molecules; catalysis; materials science; molecular modelling and simulations; machine learning tools
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Special Issue Information

Dear Colleagues,

This Special Issue commemorates the 25th anniversary of the International Journal of Molecular Sciences (IJMS), celebrating a quarter-century of pioneering research in the molecular sciences. We invite submissions that reflect on major advances in molecular informatics over this period and highlight emerging directions for the field. As molecular data continues to grow exponentially, molecular informatics plays a critical role in decoding complex biological and chemical systems, accelerating discovery, and fostering innovation.

This Special Issue aims to provide a comprehensive overview of current methodologies, applications, and theoretical developments. We encourage contributions that demonstrate the impact of molecular informatics across a wide range of areas, including drug discovery, materials science, systems biology, and the integration of artificial intelligence in molecular research. Join us in celebrating this milestone by sharing your innovative work and shaping the future of molecular informatics.

Dr. M. Natália D.S. Cordeiro
Prof. Dr. Giulio Vistoli
Guest Editors

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. 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

  • AI-guided drug repurposing
  • virtual screening in personalized medicine
  • machine learning for toxicity prediction
  • network-based biomarkers in complex diseases
  • in silico pharmacokinetics and ADMET profiling
  • data-driven materials design
  • deep learning for molecular property prediction
  • AI-assisted nanomaterial synthesis
  • systems biology models for metabolic engineering

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Published Papers (1 paper)

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Research

23 pages, 4383 KB  
Article
Gaussian Accelerated Molecular Dynamics Simulations Combined with NRIMD to Explore the Mechanism of Substrate Selectivity of Cid1 Polymerase for Different Nucleoside Triphosphates
by Hanwen Liu, Xue Zhou, Haohao Wang, Fuyan Cao and Weiwei Han
Int. J. Mol. Sci. 2025, 26(19), 9325; https://doi.org/10.3390/ijms26199325 - 24 Sep 2025
Abstract
Cid1 protein is a crucial component in the RNA interference pathway and abnormal nuclear RNA turnover processes, primarily responsible for adding uridine to the 3′ end of RNA. Cid1 exhibits selective polymerization of UTP over other nucleoside triphosphates. To explore the mechanism of [...] Read more.
Cid1 protein is a crucial component in the RNA interference pathway and abnormal nuclear RNA turnover processes, primarily responsible for adding uridine to the 3′ end of RNA. Cid1 exhibits selective polymerization of UTP over other nucleoside triphosphates. To explore the mechanism of this selectivity, five systems: free-Cid1, Cid1-ATP, Cid1-UTP, Cid1-CTP, and Cid1-GTP with 500 ns Gaussian accelerated molecular dynamics (GaMD) simulations were performed to investigate conformational changes and binding affinities between substrates and Cid1. The results showed that UTP formed stronger and more numerous non-covalent interactions with Cid1 compared to the other three substrates. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energy analysis revealed a substrate preference for Cid1 polymerase in the order of UTP, followed by ATP, CTP, and GTP. These findings provide theoretical insights into the substrate selectivity mechanism of Cid1 and provide theoretical clues for the design and modification of Cid1 polymerase. Full article
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