FAPS: A Fast Platform for Protein Structureomics Analysis
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arXiv
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| Main Authors: | , , , , , , , , , |
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866911000622530560 |
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| author | Wilken, Lucas Paul, Nihjum Timmerman, Troy Tolba, Sara A. Arshad, Amara Wu, Di Xia, Wenjie Rasulev, Bakhtiyor Jansen, Rick Sun, Dali |
| author_facet | Wilken, Lucas Paul, Nihjum Timmerman, Troy Tolba, Sara A. Arshad, Amara Wu, Di Xia, Wenjie Rasulev, Bakhtiyor Jansen, Rick Sun, Dali |
| contents | Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have become pervasive in cancer biology studies and reach well beyond more specialized areas such as metabolomics, epigenomics, pharmacogenomics, and interact-omics. However, large-scale analysis based on the structure of the biomolecules, namely structure-omics, is still underexplored due to a lack of handy tools. In response, we developed the Fast Analysis of Protein Structure (FAPS) database, a platform designed to advance quantitative proteomics to structure-omics analysis, which significantly shortens large-scale structure-omics from weeks to seconds. FAPS can serve as a new protein secondary structure database, providing a centralized and functional database for both simulated and experimentally determined bioinformatics statistics relating to secondary structure. Stored data is generated both through the structure simulation, currently SWISS-MODEL and AlphaFold, performed by high-performance computers, and the pre-existing UniProt database. FAPS provides user-friendly features that create a straightforward and effective way of accessing accurate data on the proportion of secondary structure in different protein chains, providing a fast numerical and visual reference for protein structure calculations and analysis. FAPS is accessible through http://fapsdb.org. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2506_10134 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | FAPS: A Fast Platform for Protein Structureomics Analysis Wilken, Lucas Paul, Nihjum Timmerman, Troy Tolba, Sara A. Arshad, Amara Wu, Di Xia, Wenjie Rasulev, Bakhtiyor Jansen, Rick Sun, Dali Quantitative Methods Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have become pervasive in cancer biology studies and reach well beyond more specialized areas such as metabolomics, epigenomics, pharmacogenomics, and interact-omics. However, large-scale analysis based on the structure of the biomolecules, namely structure-omics, is still underexplored due to a lack of handy tools. In response, we developed the Fast Analysis of Protein Structure (FAPS) database, a platform designed to advance quantitative proteomics to structure-omics analysis, which significantly shortens large-scale structure-omics from weeks to seconds. FAPS can serve as a new protein secondary structure database, providing a centralized and functional database for both simulated and experimentally determined bioinformatics statistics relating to secondary structure. Stored data is generated both through the structure simulation, currently SWISS-MODEL and AlphaFold, performed by high-performance computers, and the pre-existing UniProt database. FAPS provides user-friendly features that create a straightforward and effective way of accessing accurate data on the proportion of secondary structure in different protein chains, providing a fast numerical and visual reference for protein structure calculations and analysis. FAPS is accessible through http://fapsdb.org. |
| title | FAPS: A Fast Platform for Protein Structureomics Analysis |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2506.10134 |