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University of Colorado Denver

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Computational Chemistry and Biology Core Facility

Macromolecule Modeling and Analysis


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Determining the structure and properties of a macromolecule, such as enzymes, antibodies, DNA, or RNA, is fundamental to understanding structure-activity relationships, protein-protein interactions, DNA/RNA binding, and small molecule design.  The CCB Core utilizes validated scientific tools to aid in every step of macromolecule research.  Services include:

  • Protein sequence analysis of enzymes, antibodies, and multiple chain proteins
    • Protein sequence alignment
    • Secondary structure prediction
    • Transmembrane segment prediction
    • Phylogenic / evolutionary trace analysis
  • 3D structure generation of macromolecules
    • Analysis and cleaning of models from 3D structure databases (PDB, etc.)
    • Construction and evaluation of protein homology models when X-ray/NMR data is unavailable.
    • Antibody loop refinement, loop grafting, or ab initio loop modeling
    • Protein side-chain and loop conformation prediction and optimization
  • Predicting macromolecule interactions
    • Protein-protein docking and binding partner/interaction interface prediction
    • DNA/RNA-ligand, protein-ligand, and protein-DNA/RNA interactions
    • Transmembrane protein interaction with lipid membranes
    • Antigen-antibody docking
  • Predicting effects of amino acid mutations or modifications on macromolecule properties
    • Structural alterations
    • Impact on binding affinity and protein-protein interactions
    • Effects on protein stability
    • Potential for protein aggregation