Publications by authors named "Pek U Ieong"

Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and occasional pandemic outbreaks. Influenza neuraminidase, a viral surface glycoprotein, has two sialic acid binding sites. The catalytic (primary) site, which also binds inhibitors such as oseltamivir carboxylate, is responsible for cleaving the sialic acid linkages that bind viral progeny to the host cell.

View Article and Find Full Text PDF

Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing.

View Article and Find Full Text PDF

Studies of pathogen-host specificity, virulence, and transmissibility are critical for basic research as well as for assessing the pandemic potential of emerging infectious diseases. This is especially true for viruses such as influenza, which continue to affect millions of people annually through both seasonal and occasional pandemic events. Although the influenza virus has been fairly well studied for decades, our understanding of host-cell binding and its relation to viral transmissibility and infection is still incomplete.

View Article and Find Full Text PDF

The "guardian of the genome", p53, functions as a tumor suppressor that responds to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Mutation of p53 disrupts its tumor suppressor function, leading to various types of human cancers. One particular mutant, R175H, is a structural mutant that inactivates the DNA damage response pathway and acquires oncogenic functions that promotes both cancer and drug resistance.

View Article and Find Full Text PDF

With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine.

View Article and Find Full Text PDF

We describe the development of automated workflows that support computed-aided drug discovery (CADD) and molecular dynamics (MD) simulations and are included as part of the National Biomedical Computational Resource (NBCR). The main workflow components include: file-management tasks, ligand force field parameterization, receptor-ligand molecular dynamics (MD) simulations, job submission and monitoring on relevant high-performance computing (HPC) resources, receptor structural clustering, virtual screening (VS), and statistical analyses of the VS results. The workflows aim to standardize simulation and analysis and promote best practices within the molecular simulation and CADD communities.

View Article and Find Full Text PDF