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