CCD2

CCD2 automates design of protein-truncation constructs for recombinant expression by integrating sequence conservation, secondary structure prediction, domain identification, disorder detection, post-translational modification annotation, and Protein Data Bank (PDB) domain structure data.

Key Features:

• Data Aggregation: Aggregates sequence conservation analysis, secondary structure prediction, domain(s) identification, disorder detection, post-translational modification annotations, and related domain structures from the Protein Data Bank (PDB).
• Construct Boundary Selection: Selects and proposes construct boundaries informed by structural and functional domain annotations.
• Primer Design Automation: Generates primers for amplification of defined constructs by polymerase chain reaction (PCR).
• Construct Analysis: Performs rapid analysis of selected construct properties relevant to expression and experimental suitability.
• DNA Vector Mapping: Produces DNA vector maps corresponding to designed constructs.

Scientific Applications:

• Recombinant protein production: Designs truncation constructs for recombinant protein expression and production workflows.
• Structural biology studies: Optimizes constructs for structural biology experiments requiring precise structural analysis of proteins.
• Functional domain characterization: Facilitates generation of truncation constructs to investigate protein domains and functional regions.

Methodology:

Aggregates conservation, secondary structure, domain, disorder and post-translational modification data alongside PDB domain structure information; selects construct boundaries; generates PCR primers; analyzes construct properties; and generates DNA vector maps.