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After AlphaFold2: Exploring beyond Its Limits
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After AlphaFold2: Exploring beyond Its Limits

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 4630

Special Issue Editor

Prof. Dr. Ho-Jin Lee

E-Mail Website
Guest Editor
Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN 38103, USA
Interests: protein folding; foldamer; modeling; fluorescence; AlphaFold2

Special Issue Information

Dear Colleagues,

AlphaFold2(AF2) has an enormous impact on the scientific and medical fields. AF2 can predict the three-dimensional structures of proteins from their primary amino acid sequence at high accuracy. Despite the achievement of significant breakthroughs, there is still room for development. Researchers have recognized the limitations of AF2, reporting that the prediction of the effect of missense mutations on proteins and conformational changes of proteins upon binding ions (or ligands) is challenged. For example, kinases play essential roles in cellular signaling and in diseases. The accuracy of their structural information is important for drug discovery and development. However, the prediction of conformational changes of kinases by AF2, so-called open and closed conformations, need to be approached in a cautious manner.

In this Special Issue, we aim to collect new research and reviews that highlight any efforts to overcome AF2’s limitations and the next generation of algorithms. In addition, the application of AF2 in predicting membrane proteins, kinases, and intrinsically disordered proteins (IDPs), and designing de novo proteins is encouraged.    

Prof. Dr. Ho-Jin Lee
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

  • AlphaFold2
  • AF2
  • kinases
  • SNP
  • conformational change
  • membrane
  • GPCR
  • ion and ligand binding
  • algorithm

Published Papers (1 paper)

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Research

17 pages, 6336 KiB  
Article
Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold
by Takatsugu Kosugi and Masahito Ohue
Int. J. Mol. Sci. 2023, 24(17), 13257; https://doi.org/10.3390/ijms241713257 - 26 Aug 2023
Cited by 4 | Viewed by 4277
Abstract
More than 930,000 protein–protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting PPIs, but it is difficult [...] Read more.
More than 930,000 protein–protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting PPIs, but it is difficult to predict the structure of a target protein–cyclic peptide complex or to design a cyclic peptide sequence that binds to the target protein using computational methods. Recently, AlphaFold with a cyclic offset has enabled predicting the structure of cyclic peptides, thereby enabling de novo cyclic peptide designs. We developed a cyclic peptide complex offset to enable the structural prediction of target proteins and cyclic peptide complexes and found AlphaFold2 with a cyclic peptide complex offset can predict structures with high accuracy. We also applied the cyclic peptide complex offset to the binder hallucination protocol of AfDesign, a de novo protein design method using AlphaFold, and we could design a high predicted local-distance difference test and lower separated binding energy per unit interface area than the native MDM2/p53 structure. Furthermore, the method was applied to 12 other protein–peptide complexes and one protein–protein complex. Our approach shows that it is possible to design putative cyclic peptide sequences targeting PPI. Full article
(This article belongs to the Special Issue After AlphaFold2: Exploring beyond Its Limits)
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