Exploring the Chemical Space of Antiparasitic Peptides and Discovery of New Promising Leads through a Novel Approach based on Network Science and Similarity Searching - Supporting Information
Creators: name: Ayala-Ruano, Sebastián
name: Marrero-Ponce, Yovani
name: Aguilera‑Mendoza, Longendri
name: Pérez, Noel
name: Agüero-Chapin, Guillermin
name: Antunes, Agostinho
name: Aguilar, Ana Cristina
Publisher: name: Zenodo
Year: 2021
Subjects: subject: Antimicrobial peptides
subject: Antiparasitic peptides
subject: Network science
subject: Similarity searching
subject: StarPepDB
subject: StarPep Toolbox
subject: Cheminformatics
subject: Bioinformatics
subject: FOS: Computer and information sciences

description: Supporting Information for a draft of the article titled <em>Exploring the Chemical Space of Antiparasitic Peptides and Discovery of New Promising Leads through a Novel Approach based on Network Science and Similarity Searching. </em> We explain the contents of this material below: <strong>Supporting information 1 (SI1): </strong>FASTA files of 550, 415, and 405 antiparasitic peptides (APPs) to generate networks for this study. Also, this folder contains FASTA files of the five benchmarking datasets of APPs/non-APPs used to compare the performance of our multi-query similarity searching models (mQSSMs) between them and with the algorithms previously reported in the literature. <strong>Supporting information 2 (SI2): </strong>MS word file with tables of parameters of similarity threshold analysis for chemical space networks (CSNs) and half-space proximal networks (HSPNs) of APPs; common APPs in the top 50 of most central nodes from CSN and HSPN retrieved by weighted degree, hub-bridge, harmonic, and betweenness centrality measures; the number and community membership percentage of the most central APPs by weighted degree, hub-bridge, harmonic, and betweenness centrality measures; and query sets and the number of queries from the mQSSMs to find novel APPs for CSN, HSPN, and CSN-HSPN. <strong>Supporting information 3</strong> <strong>(SI3): </strong>Graphml files of all the networks created in this study. <strong>Supporting information 4 (SI4): </strong>Excel file with normalized weighted degree, hub-bridge, harmonic, and betweenness centrality measures for CSN and HSPN. <strong>Supporting information 5 (SI5): </strong>FASTA files of the most central and non-redundant APPs by each type of network and centrality measures, or the query sets. <strong>Supporting information 6 (SI6): </strong>Excel files with results of mQSSMs (Output Predictions). <strong>Supporting information 7 (SI7): </strong>This folder has three kinds of files, SI7-A that contains three folders with original results for each mQSSM generated, as well an excel file with statistical parameters. SI7-B is an excel file with the performance parameter of the best 21 mQSSMs proposed, as well as the ranking of these models. Finally, SI7-C and SI7-D are pdf files with results of multiple comparisons of our mQSSMs and with literature algorithms, respectively. <strong>Supporting information 8 (SI8)</strong>: FASTA files of 95 lead compounds and communities obtained from the CSN of these compounds. <strong>Supporting information 9 (SI9)</strong>: PowerPoint file with alignments and sequence logos of 95 lead compounds and communities obtained from the CSN of these peptides.