Translational Cancer Bioinformatics

The rise in use of "–omics" techniques to develop effective cancer therapies, in particular the Cancer Genome Atlas project (TCGA,, has demonstrated the significant role of computational and informational science in the study and treatment of cancer. It is with the tremendous significance of such topics in mind that this symposium was organized. Four speakers, Drs. Carlos J. Camacho (Computational and Systems Biology, University of Pittsburgh), Wenyuan  Li (Molecular and Computational Biology, University of Southern California), Iwona Weidlich (CODDES LLC, Rockville, MD), and Shuxing Zhang (Department of Experimental Therapeutics, MD Anderson Cancer Center), delivered excellent presentations covering diverse aspects of ongoing research topics in this area.

Dr. Carlos Camacho (University of Pittsburg) discussed New chemistry and powerful interactive technologies to discover PPI antagonists,” focusing on his group’s development of computational tools for rational design of protein-protein inhibitors of critical cancer targets. He also discussed implementation and use of Pocket Query (, a web-based tool for identification of hot spots and binding pockets defined by clusters of residues at the interface of protein-protein interactions. This method can be used for virtual screening and computational design of protein-protein interaction inhibitors. The methodology has been extended to the development of Anchor Query (, an interactive tool for rational design of protein-protein interaction inhibitors through the use of defined pharmacophores and conformational searching. This methodology has been applied to the MDM2/p53 system and other cancer targets.

Dr. Wenyuan Li (University of Southern California, Los Angeles) presented his work in Dr. Jasmin Zhou’s group (, “Integrative analysis of multidimensional cancer genomics data,” focusing on  the development  of software tools and analytical methods to analyze the multi-dimensional ovarian cancer data from the TCGA project, including the copy number variation, DNA methylation, gene expression, and microRNA expression data. Using their methodology, termed Sparse Multi-Block PLS regression, they have successfully identified pathways and associations that would have been overlooked with only a single type of data.  Their software is useful for recognizing hidden patterns and biological implications in multi-dimensional “-omics” data.

Dr. Iwona Weidlich (CODDES), with a title of “New application to estimate the diversity of molecular databases,” discussed Diversity Genie ( ), a set of computational tools useful for analysis of small organic molecule datasets to understand and characterize the diversity in the chemical space. The package can also be employed to sort, merge, and handle large sets of small organic molecules, including conversion between different data formats (e.g., SMILES, InChI, SDF, etc.) and filtering based on chemical and structural properties along with visualization.

Dr. Shuxing Zhang (MD Anderson Cancer Center) completed the symposium with “Computational analysis of pleckstrin homology (PH) domains for cancer drug development,” (, a very specific example of rationally designing inhibitors for targeted cancer therapies using integrated cheminformatics, bioinformatics, and systems biology approaches.

The pleckstrin homology (PH) domain is critical in more than 250 families of proteins involved in intracellular signaling and molecular recognitions. For instance, the PH domain plays a critical role in recruiting oncogene proteins (e.g., Akt) to the membranes for their activation contributing to cancer cell growth. As the 3D folds of PH domains are highly conserved and individual PH domains possess different affinities and specificities for a variety of phosphoinositides, genomics and bioinformatics analyses, along with structure-based methods, and can play a significant role in the rational design of selective inhibitors of these crucial cancer signaling proteins. The integrated approaches developed by this group have been rigorously cross-validated with  a large set of PH domain structures, and it was successfully applied to the prediction of several PH domain proteins, followed by discovery of potent PH domain inhibitors (

In summary, the symposium covered diverse topics from development of useful software for identifying genomic mutations in cancer pathways, to analysis and manipulation of small organic molecules, and to the rational design of promising therapeutics for targeted cancer therapies.

Rachelle Bienstock and Shuxing Zhang, Symposium Organizers



Oral presentations captured at the ACS Spring National Meeting in Dallas will be available to ACS Members after April 28, 2014 at

The following presentation was recorded at the “Translational Cancer Bioinformatics Data, Methods and Applications” symposium:

CINF23 New application to estimate the diversity of molecular databases. Iwona Weidlich


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