MOTIVATION: Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the ove...
MOTIVATION: Understanding the specificity of protein receptor-ligand interactions is pivotal for our comprehension of biological mechanisms and systems. Receptor protein families often have a certain level of sequence diversity that converges into fe...
SUMMARY: TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable...
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: 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...
MOTIVATION: In bioinformatics, machine learning-based methods that predict the compound-protein interactions (CPIs) play an important role in the virtual screening for drug discovery. Recently, end-to-end representation learning for discrete symbolic...
The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product...
Database : the journal of biological databases and curation
Jan 1, 2019
The scientific literature contains large amounts of information on genes, proteins, chemicals and their interactions. Extraction and integration of this information in curated knowledge bases help researchers support their experimental results, leadi...
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 ...
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