Database : the journal of biological databases and curation
30239677
In the era of data explosion, the increasing frequency of published articles presents unorthodox challenges to fulfill specific curation requirements for bio-literature databases. Recognizing these demands, we designed a document triage system with a...
Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational space of the...
MOTIVATION: Many inference problems in bioinformatics, including drug bioactivity prediction, can be formulated as pairwise learning problems, in which one is interested in making predictions for pairs of objects, e.g. drugs and their targets. Kernel...
Journal of computer-aided molecular design
30116918
Advanced mathematics, such as multiscale weighted colored subgraph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affin...
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...
Noncovalent inhibitors of protein kinases have different modes of action. They bind to the active or inactive form of kinases, compete with ATP, stabilize inactive kinase conformations, or act through allosteric sites. Accordingly, kinase inhibitors ...
The kinome-wide virtual profiling of small molecules with high-dimensional structure-activity data is a challenging task in drug discovery. Here, we present a virtual profiling model against a panel of 391 kinases based on large-scale bioactivity dat...
Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to functional ac...
Early identification of metastatic or recurrent colorectal cancer (CRC) patients who will be sensitive to FOLFOX (5-FU, leucovorin and oxaliplatin) therapy is very important. We performed microarray meta-analysis to identify differentially expressed ...
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describ...