APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design

Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity prediction. However, these methods are usually trained on only ligand bound (or holo) conformations of the protein and therefore are not guaranteed to perform well when the protein structure is in its native unbound conformation (or apo), which is usually the conformation available for a newly identified receptor. A primary reason for this is that the local structure of the binding site usually changes upon ligand binding. To facilitate solutions for this problem, we propose a dataset called APObind that aims to provide apo conformations of proteins present in the PDBbind dataset, a popular dataset used in drug design. Furthermore, we explore the performance of methods specific to three use cases on this dataset, through which, the importance of validating them on the APObind dataset is demonstrated.

MMBERT: Multimodal BERT Pretraining for Improved Medical VQA

Images in the medical domain are fundamentally different from the general domain images. Consequently, it is infeasible to directly employ general domain Visual Question Answering (VQA) models for the medical domain. Additionally, medical images annotation is a costly and time-consuming process. To overcome these limitations, we propose a solution inspired by self-supervised pretraining of Transformer-style architectures for NLP, Vision and Language tasks. Our method involves learning richer medical image and text semantic representations using Masked Language Modeling (MLM) with image features as the pretext task on a large medical image+caption dataset. The proposed solution achieves new state-of-the-art performance on two VQA datasets for radiology images -- VQA-Med 2019 and VQA-RAD, outperforming even the ensemble models of previous best solutions. Moreover, our solution provides attention maps which help in model interpretability. The code is available at https://github.com/VirajBagal/MMBERT