Center Capabilities

Assay Design

  • Biochemical assays
  • Cell-based assays
  • Image-based assays
  • Whole organism-based assays

NIH Chemical Genomics Assay Guidance Manual including a chapter on inhibition of protein-protein interactions by ECBDC Associate Director, Yuhong Du

High-Throughput Screening

Screening Systems

We have established multiple independent, parallel robotic systems for HTS/μHTS/iHTS and HCS operations that are capable of handling 96-, 384-, and 1536-well plate formats. These systems accommodate a variety of assay formats and are particularly well-suited for conventional and multiplex protein-protein interactions and phenotypic screens.

  • HTS/HCS system I: The first system features a central vertical robotic system with three outpost readers: (i) EnVision multimode reader (HTS in 96/384/1536 well format), (ii) FlexStation II agonist-injectable, 384-well fluorescence reader, and (iii) ImageXpress (HCS in 96/384-well format). This system is integrated with a cell hotel, plate stacker, and various liquid handlers equipped with pin tools for low-volume (nL) transfer. All of these components are in an enclosed environment, facilitating live-cell HCS screens under aseptic conditions.
  • HTS/HCS system II: The second system features the Twister II robot integrated with (i) an EnVision multimode reader (HTS in 96/384/1536-well format) and (ii) ImageXpress (HCS in 96/384/1536 well format) supported by the Sciclone liquid handling workstation.
  • System III: Corning’s Epic system for label-free molecular interaction screens provides a third platform for hit identification and confirmation by direct detection of protein-compound binding and cell-based screens under physiological conditions.

Compound library collections

We have a collection of more than 500K chemical compounds, including:

  • Bioactive compounds
  • FDA approved drugs
  • Natural products
  • Diversity libraries


High-throughput screening data analysis and management

  • Data reduction and management
  • Data presentation, result query
  • Compound library management, plate managment
  • File preprocessing, report preparation
  • Chemical queries


  • Cluster analysis and hit-prioritization
  • Molecular property calculations and filtering
  • PAINS and REOS compounds identification
  • Quantitative Structure-Activity Relationship (QSAR)
  • ADME properties prediction


  • Integration and analysis of large-scale genomic datasets, including
    • NCI Genomic Data Commons
    • The Cancer Genome Atlas (TCGA)
    • Cancer Cell Line Encyclopedia (CCLE)
    • Project Achilles
  • Analysis of gene co-expression and mutual exclusivity of genomic alterations
  • Analysis of Protein-protein, protein-compound, and functional interaction networks topology

Molecular Modeling

  • Protein homology modeling, analysis of secondary structure, and functional domains
  • Molecular docking and virtual screening of compound libraries
  • Protein-protein and protein-peptide docking
  • Molecular dynamics simulation
  • Structure-based and ligand-based drug design and structure optimization