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Computational Approaches for the Investigation of Complex Molecular Mechanisms 3.0

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: 10 October 2024 | Viewed by 392

Special Issue Editor


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Guest Editor
Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
Interests: signal transduction; calcium; molecular modeling; molecular dynamics; docking; mathematical modeling
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Special Issue Information

Dear Colleagues,

In recent years, technical and scientifical progress in computational science has provided valuable and affordable tools for scientific research in the field of molecular biology. From bioinformatics to molecular modeling, from the -omics approach to the development of mathematical models, computational biomodeling has provided relevant contributions to the clarification of fundamental biological mechanisms.

For this Special Issue, we would like to invite papers that address the following concepts:

  • Integrated approach between wet and in silico techniques to tackle a relevant biological issue;
  • Exploitation of computational models to direct wet research;
  • Computational approach applied to gain novel interpretation of previous experimental data.

Suggested methodologies include, but are not limited to, bioinformatics, homology modelling, analysis of gene expression to identify transcriptional regulation pathways, protein–protein and ligand–protein docking, molecular dynamics, mathematical modeling, and molecular or cell biology techniques (not mandatory).

Dr. Renata Tisi
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. 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

  • signal transduction
  • transcriptional regulation
  • molecular modeling
  • molecular dynamics
  • molecular docking
  • system biology
  • mathematical modeling
  • meta-analysis

Published Papers (1 paper)

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Research

23 pages, 3142 KiB  
Article
ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins
by Tao Ma, Wenhui Li, Zhiping Tang, Xiangwei Sun, Lijuan Li, Zhonghua Liu and Gaihua Zhang
Int. J. Mol. Sci. 2024, 25(10), 5176; https://doi.org/10.3390/ijms25105176 - 9 May 2024
Viewed by 251
Abstract
The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact [...] Read more.
The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue–residue contacts in NMR structures of P4HB, protein–drug binding of CYP17A1, protein–DNA binding of SPI1, and molecular dynamic simulations of BRD4. Full article
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