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Recent Advances in Protein Bioinformatics

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (5 May 2021) | Viewed by 2919

Special Issue Editors


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Guest Editor
Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, 35121 Padua, Italy
Interests: structural bioinformatics; intrinsically disordered proteins; machine learning

E-Mail Website
Guest Editor
Department of Biomedical Sciences – DSB,University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy
Interests: proteins; bioinformatics and computational biology; bioinformatics; protein structure; proteomics; computational biology; biostatistics; JavaScript; structural biology; Python scripting
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I would like to invite you to submit a contribution to a Special Issue of Applied Sciences entitled “Recent Advances in Protein Bioinformatics”.

Bioinformatics, or the development of computational methods for understanding biological data, has seen a surge of energy in recent years. The understanding of protein structure and function has vastly benefitted from new models, methods, and tools. This revolution has mainly been fueled by an ever-increasing computational power, giving access to previously unthinkable calculations as in the case of molecular dynamics pushing the boundaries of microseconds; advanced machine-learning techniques modeling complex problems, as in the case of AlphaFold, Google’s deep-neural-network algorithm for de novo prediction of protein folding; and mathematical approaches applied to complex problems from a different perspective, as in the case of RING, which analyzes amino-acid contacts exploiting graph theory. The added value deriving from the combined approach of biochemistry and computer science reflects the deep interdisciplinarity of the problems arising in the field of protein biochemistry, and the rise in mixed approaches is a trend destined to soar in the coming years.

Dr. Marco Necci
Dr. Lisanna Paladin
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. Applied Sciences is an international peer-reviewed open access semimonthly 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 2400 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

  • graph theory
  • molecular dynamics
  • neural-networks
  • machine learning
  • intrinsic disorder
  • protein folding
  • protein function
  • high-performance computing

Published Papers (1 paper)

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Research

29 pages, 8255 KiB  
Article
Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases
by Mateusz Banach, Jacques Chomilier and Irena Roterman
Appl. Sci. 2021, 11(18), 8514; https://doi.org/10.3390/app11188514 - 14 Sep 2021
Cited by 4 | Viewed by 2269
Abstract
Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via [...] Read more.
Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in their monomeric and dimeric forms are the object of this work. Characteristic of hydrophobic core in both molecules is analyzed via fuzzy oil drop model (FOD) to show the specificity of their structure enabling the binding of a relatively large ligand and formation of the complex. Structures of FdI and FdII are a promising example for the discussion of influence of hydrophobicity on biological activity but also for an explanation how FOD model can be used as an initial stage adviser (or a scoring function) in the search for locations of ligand binding pockets and protein–protein interaction areas. It is shown that observation of peculiarities in the hydrophobicity distribution present in the molecule (in this case—of a ferredoxin) may provide a promising starting location for computer simulations aimed at the prediction of quaternary structure of proteins. Full article
(This article belongs to the Special Issue Recent Advances in Protein Bioinformatics)
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