Intermolecular Interactions in Macromolecular Complexes

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Macromolecular Crystals".

Deadline for manuscript submissions: 15 June 2024 | Viewed by 776

Special Issue Editors


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Guest Editor
Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama 226-8501, Japan
Interests: bioinformatics; cheminformatics; protein–protein interaction; protein–ligand interaction; structure-based drug discovery; machine learning; chemical language model; peptide design; alphafold

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Guest Editor
1. Department of Chemistry, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy
2. Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
Interests: structural biology; protein crystallography; protein crystals; protein engineering

Special Issue Information

Dear Colleagues,

We are delighted to announce a new Special Issue, "Intermolecular Interactions in Macromolecular Complexes". The interactions within molecular complexes play a crucial role in a multitude of chemical and biological phenomena, such as the understanding and generation of high-functionality complexes, the regulation of biological functions, and the comprehension of diseases.

For this Special Issue, we aim to compile pioneering work that enhances our understanding of these interactions, particularly through cutting-edge experimental approaches that shed light on new phenomena. Of particular interest is the recent rapid advancement of computational technologies for molecular structures, exemplified by the likes of AlphaFold. The development and application of computational prediction technologies are vital areas we wish to explore.

Furthermore, we highly anticipate contributions that leverage machine learning and AI technology, including deep learning, which promise rich insights and breakthrough results in the field. We invite original research articles, reviews, and communications that capture the innovative spirit of this research area.

Join us in this exciting endeavor to decipher the intricate tapestry of intermolecular interactions in macromolecular complexes.

Dr. Masahito Ohue
Prof. Dr. Oliviero Carugo
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. Crystals is an international peer-reviewed open access monthly 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 2600 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

  • macromolecular complexes
  • protein assembly
  • protein–protein/DNA/RNA/ligand interactions
  • structural biology
  • structure-based drug discovery
  • computational biology/chemistry
  • machine learning/artificial intelligence

Published Papers (1 paper)

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Review

14 pages, 1612 KiB  
Review
B-Factor Rescaling for Protein Crystal Structure Analyses
by Georg Mlynek, Kristina Djinović-Carugo and Oliviero Carugo
Crystals 2024, 14(5), 443; https://doi.org/10.3390/cryst14050443 - 7 May 2024
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Abstract
The B-factor, also known as the atomic displacement parameter, is a fundamental metric in crystallography for quantifying the positional flexibility of atoms within crystal lattices. In structural biology, various developments have expanded the use of B-factors beyond conventional crystallographic analysis, allowing for a [...] Read more.
The B-factor, also known as the atomic displacement parameter, is a fundamental metric in crystallography for quantifying the positional flexibility of atoms within crystal lattices. In structural biology, various developments have expanded the use of B-factors beyond conventional crystallographic analysis, allowing for a deeper understanding of protein flexibility, enzyme manipulation, and an improved understanding of molecular dynamics. However, the interpretation of B-factors is complicated by their sensitivity to various experimental and computational factors, necessitating rigorous rescaling methods to ensure meaningful comparisons across different structures. This article provides an in-depth description of rescaling approaches used for B-factors. It includes an examination of several methods for managing conformational disorder and selecting the atom types required for the analysis. Full article
(This article belongs to the Special Issue Intermolecular Interactions in Macromolecular Complexes)
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