Pharmacogenomic studies are studies designed to elucidate the relationships between drugs and genes on the genomic scale. Given the rapidly increasing amount of microarray data in international repositories, and the implicit drug information contained in PubMed, MeSH and UMLS, we propose automatic methods for identifying drug-related microarray experiments from NCBI GEO by the semantic connections between these data resources. In our study, we...

The amount of gene expression data in international repositories has grown exponentially. An important first step in translating the results of genomic experiments into medicine is to relate these genomic experiments to the human diseases they have studied. Unfortunately, repositories for expression data store the crucial annotative details only as free-text, making it manually intractable to link these with human disease. In this study, we...

We present an evaluation of the results of our ZDOCK and RDOCK algorithms in Rounds 3, 4, and 5 of the protein docking challenge CAPRI. ZDOCK is a Fast Fourier Transform (FFT)-based, initial-stage rigid-body docking algorithm, and RDOCK is an energy minimization algorithm for refining and reranking ZDOCK results. Of the 9 targets for which we submitted predictions, we attained at least acceptable accuracy for 7, at least medium accuracy for 6,...

We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with...

We present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid-body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three-stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimization, and reverted to their full charge states in the...