Exploiting PubChem for virtual screening

Virtual Screening and Docking Studies of Selected Pubchem Compounds

Benchmarking ligand-based virtual High-Throughput Screening with the PubChem database.

With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families o...

QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem

Many of the structures in PubChem are annotated with activities determined in high-throughput screening (HTS) assays. Because of the nature of these assays, the activity data are typically strongly imbalanced, with a small number of active compounds contrasting with a very large number of inactive compounds. We have used several such imbalanced PubChem HTS assays to test and develop strategies ...

Exploiting GPUs in Virtual Machine for BioCloud

Recently, biological applications start to be reimplemented into the applications which exploit many cores of GPUs for better computation performance. Therefore, by providing virtualized GPUs to VMs in cloud computing environment, many biological applications will willingly move into cloud environment to enhance their computation performance and utilize infinite cloud computing resource while r...

A virtual file system for the PubChem chemical structure and bioassay database

The PubChem chemical structure and bioassay database (http://pubchem.ncbi.nlm.nih.gov) has established itself as one of the premier information sources for chemical structures and assay data accessible via the Internet. PubChem provides a convenient interactive Web interface for the execution and result display of standard structure and text-based queries. However, the capabilities for formulat...