MOTIVATION: Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction....
MOTIVATION: The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without so...
MOTIVATION: Structure-based drug discovery methods exploit protein structural information to design small molecules binding to given protein pockets. This work proposes a purely data driven, structure-based approach for imaging ligands as spatial fie...
Combinatorial chemistry & high throughput screening
Jan 1, 2019
AIM AND OBJECTIVE: The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding ...
MOTIVATION: Transcription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription...
SUMMARY: Convolutional neural networks (CNNs) have been shown to perform exceptionally well in a variety of tasks, including biological sequence classification. Available implementations, however, are usually optimized for a particular task and diffi...
MOTIVATION: The convolutional neural network (CNN) has been applied to the classification problem of DNA sequences, with the additional purpose of motif discovery. The training of CNNs with distributed representations of four nucleotides has successf...
The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address ...
MOTIVATION: Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally r...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2018
The increasing number of protein structures with uncharacterized function necessitates the development of in silico prediction methods for functional annotations on proteins. In this chapter, different kinds of computational approaches are briefly in...