{"id":15157758,"url":"https://github.com/smritivaidyanathan/bioaffinix","last_synced_at":"2026-02-05T18:31:30.677Z","repository":{"id":253711372,"uuid":"844278008","full_name":"smritivaidyanathan/BioAffinix","owner":"smritivaidyanathan","description":"Bio-cheminformatics project in progress to predict small molecule inhibitory potential (IC50) against 11β-HSD1","archived":false,"fork":false,"pushed_at":"2024-08-22T02:49:53.000Z","size":11,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-31T01:58:54.935Z","etag":null,"topics":["biochemistry","bioinformatics","drug-discovery","drug-protein-interactions","python","pytorch","smiles-strings"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smritivaidyanathan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-08-18T22:55:26.000Z","updated_at":"2024-08-22T02:49:56.000Z","dependencies_parsed_at":"2024-08-19T01:23:53.172Z","dependency_job_id":"f4e16abf-c9d6-485a-b746-fbf385e57ade","html_url":"https://github.com/smritivaidyanathan/BioAffinix","commit_stats":{"total_commits":7,"total_committers":2,"mean_commits":3.5,"dds":0.4285714285714286,"last_synced_commit":"1951d2b450996063ad26d6738e3dee7db9e574eb"},"previous_names":["smritivaidyanathan/bioaffinix"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smritivaidyanathan%2FBioAffinix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smritivaidyanathan%2FBioAffinix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smritivaidyanathan%2FBioAffinix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smritivaidyanathan%2FBioAffinix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smritivaidyanathan","download_url":"https://codeload.github.com/smritivaidyanathan/BioAffinix/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":237982128,"owners_count":19397202,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biochemistry","bioinformatics","drug-discovery","drug-protein-interactions","python","pytorch","smiles-strings"],"created_at":"2024-09-26T20:02:42.694Z","updated_at":"2026-02-05T18:31:30.643Z","avatar_url":"https://github.com/smritivaidyanathan.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioAffinix\nA \"bio-cheminformatics\" project in progress to predict small molecule-protein interaction strength through a neural net trained on existing interactions from ChEMBL, amino acid sequences, and SMILES strings for a small set of proteins.\n\n**11β-Hydroxysteroid Dehydrogenase Type 1 (11β-HSD1)** is an enzyme crucial for regulating cortisol, a hormone involved in metabolism, immune response, and stress regulation. Overactivity of 11β-HSD1 is linked to metabolic syndrome, obesity, type 2 diabetes, and inflammation, making it a key target for therapeutic interventions.\n\nThis personal project aims to predict the inhibitory potential of small molecules against 11β-HSD1, which could be valuable for drug development. The model will take the molecular structure of small molecules as input and output a measure of their inhibitory power against 11β-HSD1.\n\n**Dataset**: 4,500+ embeddings generated from SMILES strings and corresponding IC50 values.\n\n**Current Approach**: Utilizing embeddings generated from the MolecularTransformerEmbeddings pre-trained transformer (https://github.com/mpcrlab/MolecularTransformerEmbeddings.git) and training a CNN with Adam Optimizer to predict IC50 values. (Reference: \"Predicting Binding from Screening Assays with Transformer Network Embeddings\")\n\n**References**\nMorris P, St Clair R, Barenholtz E, Hahn WE. Predicting Binding from Screening Assays with Transformer Network Embeddings. ChemRxiv. 2020; doi:10.26434/chemrxiv.11625885.v1 This content is a preprint and has not been peer-reviewed.\n\n\nChapman, K., Holmes, M., \u0026 Seckl, J. (2013). 11β-Hydroxysteroid dehydrogenases: intracellular gate-keepers of tissue glucocorticoid action. Physiological Reviews, 93(3), 1139-1206. DOI: 10.1152/physrev.00020.2012\n\n\nHardy, R., \u0026 Cooper, M. S. (2009). Glucocorticoid-induced osteoporosis: molecular mechanisms and therapeutic strategies. Advances in Experimental Medicine and Biology, 872, 45-58. DOI: 10.1007/978-1-4614-0432-6_3\n\n\nMorgan, S. A., McCabe, E. L., Gathercole, L. L., Hassan-Smith, Z. K., Larner, D. P., Bujalska, I. J., ... \u0026 Lavery, G. G. (2014). 11β-HSD1 is the major regulator of the tissue-specific effects of circulating glucocorticoid excess. Proceedings of the National Academy of Sciences, 111(24), E2482-E2491. DOI: 10.1073/pnas.1323681111\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmritivaidyanathan%2Fbioaffinix","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmritivaidyanathan%2Fbioaffinix","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmritivaidyanathan%2Fbioaffinix/lists"}