Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties

no code implementations • 26 Oct 2022 • Asu Büşra Temizer, Gökçe Uludoğan, Rıza Özçelik, Taha Koulani, Elif Ozkirimli, Kutlu O. Ulgen, Nilgün Karalı, Arzucan Özgür

To this end, we build a language-inspired pipeline that treats high affinity ligands of protein targets as documents and selects key chemical words making up those ligands based on tf-idf weighting.

Drug Discovery Property Prediction

Exploiting Pretrained Biochemical Language Models for Targeted Drug Design

1 code implementation • 2 Sep 2022 • Gökçe Uludoğan, Elif Ozkirimli, Kutlu O. Ulgen, Nilgün Karalı, Arzucan Özgür

On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations.