5 papers
ReACT-Drug: Reaction-Template Guided Reinforcement Learning for de novo Drug Design
R Yadunandan, Nimisha Ghosh
De novo drug design is a crucial component of modern drug development, yet navigating the vast chemical space to find synthetically accessible, high-affinity candidates remains a s…
LAMP-PRo: Label-aware Attention for Multi-label Prediction of DNA- and RNA-binding Proteins using Protein Language Models
Nimisha Ghosh, Dheeran Sankaran, Rahul Balakrishnan Adhi +2
Identifying DNA- (DBPs) and RNA-binding proteins (RBPs) is crucial for the understanding of cell function, molecular interactions as well as regulatory functions. Owing to their hi…
A Comprehensive Review of Transformer-based language models for Protein Sequence Analysis and Design
Nimisha Ghosh, Daniele Santoni, Debaleena Nawn +2
The impact of Transformer-based language models has been unprecedented in Natural Language Processing (NLP). The success of such models has also led to their adoption in other fiel…
TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites
Nimisha Ghosh, Pratik Dutta, Daniele Santoni
Transcription factors are proteins that regulate the expression of genes by binding to specific genomic regions known as Transcription Factor Binding Sites (TFBSs), typically locat…
A Review on the Applications of Transformer-based language models for Nucleotide Sequence Analysis
Nimisha Ghosh, Daniele Santoni, Indrajit Saha +1
In recent times, Transformer-based language models are making quite an impact in the field of natural language processing. As relevant parallels can be drawn between biological seq…