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Latest Review Papers in Molecular Informatics 2023
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Latest Review Papers in Molecular Informatics 2023

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: closed (28 February 2023) | Viewed by 7023

Special Issue Editor

Dr. Antonio Rescifina

E-Mail Website
Guest Editor
Department of Drug Sciences, University of Catania, 95125 Catania, Italy
Interests: organic synthesis; computational chemistry; computer aided drug design; molecular modeling; computational studies of reaction mechanisms; molecular docking; QSAR; 1,3-dipolar cycloadditions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect high-quality review papers in all the fields of molecular informatics. We encourage researchers from related fields to contribute review papers that highlight the latest developments in molecular informatics or to invite relevant experts and colleagues to do so. Full-length comprehensive reviews will be preferred.

Dr. Antonio Rescifina
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.

Published Papers (2 papers)

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11 pages, 2435 KiB  
Article
Survey of Protein Sequence Embedding Models
by Chau Tran, Siddharth Khadkikar and Aleksey Porollo
Int. J. Mol. Sci. 2023, 24(4), 3775; https://doi.org/10.3390/ijms24043775 - 14 Feb 2023
Cited by 2 | Viewed by 4662
Abstract
Derived from the natural language processing (NLP) algorithms, protein language models enable the encoding of protein sequences, which are widely diverse in length and amino acid composition, in fixed-size numerical vectors (embeddings). We surveyed representative embedding models such as Esm, Esm1b, ProtT5, and [...] Read more.
Derived from the natural language processing (NLP) algorithms, protein language models enable the encoding of protein sequences, which are widely diverse in length and amino acid composition, in fixed-size numerical vectors (embeddings). We surveyed representative embedding models such as Esm, Esm1b, ProtT5, and SeqVec, along with their derivatives (GoPredSim and PLAST), to conduct the following tasks in computational biology: embedding the Saccharomyces cerevisiae proteome, gene ontology (GO) annotation of the uncharacterized proteins of this organism, relating variants of human proteins to disease status, correlating mutants of beta-lactamase TEM-1 from Escherichia coli with experimentally measured antimicrobial resistance, and analyzing diverse fungal mating factors. We discuss the advances and shortcomings, differences, and concordance of the models. Of note, all of the models revealed that the uncharacterized proteins in yeast tend to be less than 200 amino acids long, contain fewer aspartates and glutamates, and are enriched for cysteine. Less than half of these proteins can be annotated with GO terms with high confidence. The distribution of the cosine similarity scores of benign and pathogenic mutations to the reference human proteins shows a statistically significant difference. The differences in embeddings of the reference TEM-1 and mutants have low to no correlation with minimal inhibitory concentrations (MIC). Full article
(This article belongs to the Special Issue Latest Review Papers in Molecular Informatics 2023)
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Review

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18 pages, 5293 KiB  
Review
Computer-Assisted Design of Peptide-Based Radiotracers
by Vincenzo Patamia, Chiara Zagni, Ilaria Brullo, Erika Saccullo, Alessandro Coco, Giuseppe Floresta and Antonio Rescifina
Int. J. Mol. Sci. 2023, 24(7), 6856; https://doi.org/10.3390/ijms24076856 - 06 Apr 2023
Cited by 3 | Viewed by 1767
Abstract
In medical imaging, techniques such as magnetic resonance imaging, contrast-enhanced computerized tomography, positron emission tomography (PET), and single-photon emission computed tomography (SPECT) are extensively available and routinely used for disease diagnosis. PET probes with peptide-based targeting are typically composed of small peptides especially [...] Read more.
In medical imaging, techniques such as magnetic resonance imaging, contrast-enhanced computerized tomography, positron emission tomography (PET), and single-photon emission computed tomography (SPECT) are extensively available and routinely used for disease diagnosis. PET probes with peptide-based targeting are typically composed of small peptides especially developed to have high affinity and specificity for a range of cellular and tissue targets. These probes’ key benefits include being less expensive than traditional antibody-based PET tracers and having an effective chemical modification process that allows them to be radiolabeled with almost any radionuclide, making them highly appealing for clinical usage. Currently, as with every pharmaceutical design, the use of in silico strategies is steadily growing in this field, even though it is not part of the standard toolkit used during radiopharmaceutical design. This review describes the recent applications of computational design approaches in the design of novel peptide-based radiopharmaceuticals. Full article
(This article belongs to the Special Issue Latest Review Papers in Molecular Informatics 2023)
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