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New Computational Methodologies for Biomolecule Sequence, Structure and Function Discovery

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 October 2024 | Viewed by 642

Special Issue Editor


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Guest Editor
Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
Interests: machine learning; deep learning; data mining; bioinformatics

Special Issue Information

Dear Colleagues,

With the accumulation of large-scale data in bioinformatics, researchers deal with several types of biomolecule data, such as sequences, structures, and functions. The question of how to effectively use these data in the fields of biology is an important one, as many researchers employ computational methods to analyze enzymes, identify biomolecules, biological networks, and structural proteomics, for gene expression analysis, molecular docking, post-translational modifications, etc. Many new computational methodologies have been developed for biomolecule sequence, structure, and function discovery. The novel methods presented in these studies propose new tools for tacking different problems in bioinformatics, and the new findings therein promise to provide new insights for biologists and medical scientists.

This Special Issue is focused on studies relating to novel computational methodologies and golden benchmark datasets for biomolecule sequence, structure, and function discovery. Thus, we welcome original research articles, review articles, and communications covering one or more of the following topics:

  • Bioinformatics;
  • Machine learning;
  • Deep learning;
  • Biomolecule identification;
  • Biological networks;
  • Structural proteomics;
  • Gene expression analysis;
  • Molecular docking;
  • Post-translational modifications.

Prof. Dr. Fei Guo
Guest Editor

Manuscript Submission Information

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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

  • bioinformatics
  • machine learning
  • deep learning
  • biomolecule identification
  • biological networks
  • structural proteomics
  • gene expression analysis
  • molecular docking
  • post-translational modifications

Published Papers (2 papers)

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Research

13 pages, 1732 KiB  
Article
Preimplantation Genetic Testing of Spinocerebellar Ataxia Type 3/Machado–Joseph Disease—Robust Tools for Direct and Indirect Detection of the ATXN3 (CAG)n Repeat Expansion
by Mulias Lian, Vivienne J. Tan, Riho Taguchi, Mingjue Zhao, Gui-Ping Phang, Arnold S. Tan, Shuling Liu, Caroline G. Lee and Samuel S. Chong
Int. J. Mol. Sci. 2024, 25(15), 8073; https://doi.org/10.3390/ijms25158073 - 24 Jul 2024
Viewed by 174
Abstract
Spinocerebellar ataxia type 3/Machado–Joseph disease (SCA3/MJD) is a neurodegenerative disorder caused by the ATXN3 CAG repeat expansion. Preimplantation genetic testing for monogenic disorders (PGT-M) of SCA3/MJD should include reliable repeat expansion detection coupled with high-risk allele determination using informative linked markers. One couple [...] Read more.
Spinocerebellar ataxia type 3/Machado–Joseph disease (SCA3/MJD) is a neurodegenerative disorder caused by the ATXN3 CAG repeat expansion. Preimplantation genetic testing for monogenic disorders (PGT-M) of SCA3/MJD should include reliable repeat expansion detection coupled with high-risk allele determination using informative linked markers. One couple underwent SCA3/MJD PGT-M combining ATXN3 (CAG)n triplet-primed PCR (TP-PCR) with customized linkage-based risk allele genotyping on whole-genome-amplified trophectoderm cells. Microsatellites closely linked to ATXN3 were identified and 16 markers were genotyped on 187 anonymous DNAs to verify their polymorphic information content. In the SCA3/MJD PGT-M case, the ATXN3 (CAG)n TP-PCR and linked marker analysis results concurred completely. Among the three unaffected embryos, a single embryo was transferred and successfully resulted in an unaffected live birth. A total of 139 microsatellites within 1 Mb upstream and downstream of the ATXN3 CAG repeat were identified and 8 polymorphic markers from each side were successfully co-amplified in a single-tube reaction. A PGT-M assay involving ATXN3 (CAG)n TP-PCR and linkage-based risk allele identification has been developed for SCA3/MJD. A hexadecaplex panel of highly polymorphic microsatellites tightly linked to ATXN3 has been developed for the rapid identification of informative markers in at-risk couples for use in the PGT-M of SCA3/MJD. Full article
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31 pages, 9364 KiB  
Article
Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides
by Claudiu N. Lungu, Ionel I. Mangalagiu, Gabriela Gurau and Mihaela Cezarina Mehedinti
Int. J. Mol. Sci. 2024, 25(14), 7787; https://doi.org/10.3390/ijms25147787 - 16 Jul 2024
Viewed by 331
Abstract
The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR type 2 angiogenesis and vascular morphogenesis as the tyrosine kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in [...] Read more.
The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR type 2 angiogenesis and vascular morphogenesis as the tyrosine kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in both stimulating and inhibitory ways. This investigation aims to examine the molecular properties of VEGFR2, a molecule primarily involved in the processes of vasculogenesis and angiogenesis. These relationships were defined by the interactions between Vascular Endothelial Growth Factor receptor 2 (VEGFR2) and the structural features of the systems. The chemical space of the inhibitory peptides and stimulators was described using topological and energetic properties. Furthermore, chimeric models of stimulating and inhibitory proteins (for VEGFR2) were computed using the protein system structures. The interaction between the chimeric proteins and VEGFR was computed. The chemical space was further characterized using complex manifolds and high-dimensional data visualization. The results show that a slightly similar chemical area is shared by VEGFR2 and stimulating and inhibitory proteins. On the other hand, the stimulator peptides and the inhibitors have distinct chemical spaces. Full article
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