Data file for "Vliet SMF, Hazemi M, Blatz D, Jensen M, Mayasich S, Transue TR, Simmons C, Wilkinson A, LaLone CA. Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation. J Vis Exp. 2023 Feb 10;(192). doi: 10.3791/63970. PMID: 36847398.". This dataset is associated with the following publication: Vliet, S., M. Hazemi, D. Blatz, M. Jensen, S. Mayasich, T. Transue, C. Simmons, A. Wilkinson, and C. Lalone. Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation. Journal of Visualized Experiments. JoVE, Somerville, MA, USA, 192, (2023).

The advancement of protein structural prediction tools, exemplified by AlphaFold and Iterative Threading ASSEmbly Refinement, has enabled the prediction of protein structures across species based on available protein sequence and structural data. In this study, we introduce an innovative molecular docking method that capitalizes on this wealth of structural data to enhance predictions of chemical susceptibility across species. We demonstrated this method using the androgen receptor as a pertinent modulator of endocrine function. By using protein structures, this method contextualizes species susceptibility within a functional framework and helps to integrate molecular docking into the repertoire of New Approach Methodologies (NAMs) that support the Next-Generation Risk Assessment (NGRA) paradigm through the novel integration of various open-source tools. This dataset is associated with the following publication: Schumann, P., D. Chang, S. Mayasich, S. Vliet, T. Brown, and C. LaLone. Cross-species molecular docking method to support predictions of species susceptibility to chemical effects. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 30(4): 100319, (2024).

Compute cDNA-to-Genomic sequence alignments.

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The raw data consisted of demultiplexed fastq files pairs (R1.fastq and R2.fastq) per sample accessible on the NCBI Sequences Read Archive (SRA) under the BioProject accession numbers PRJNA1187555 for experiments E1 and E3 and PRJNA1187576 for E2 and E4. This dataset is associated with the following publication: Valentin, V., S. Rivera, E. Acs, S. Almeida, K. Andree, L. Apothéloz-Perret-Gentil, B. Bailet, A. Baričević, K. Beentjes, J. Bettig, A. Bouchez, C. Camilla, C. Chardon, M. Duleba, T. Elersek, C. Genthon, M. Jablonska, L. Jacas, M. Kahlert, M. Kelly, J. Macher, F. Mauri, M. Moletta-Denat, A. Mortágua, J. Pawlowski, J. Pérez-Burillo, M. Pfannkuchen, E. Pilgrim, P. Panayiota, F. Rimet, K. Stanic, K. Tapolczai, S. Theroux, R. Trobajo, B. Van der Hoorn, M. Vasquez, M. Vidal, D. Wanless, J. Warren, J. Zimmermann, and B. Paix. Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring. Metabarcoding and Metagenomics. Pensoft Publishers, Sofia, BULGARIA, e133264, (2025).

A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages.