CoLiDe

CoLiDe generates combinatorial protein libraries by designing degenerate DNA templates with an evolutionary algorithm to explore diverse protein sequence spaces.

Key Features:

• Precision in Sequence Design: Uses an evolutionary algorithm to design degenerate DNA templates that control protein sequence composition, length, and diversity.
• Versatility Across Input Alphabets: Supports four input alphabet distributions across various sequence lengths for different design scenarios.
• High Diversity Output: Produces libraries encompassing approximately 10^11 to 10^12 unique protein sequences.
• Experimental Pipeline Integration: Includes model design and an experimental pipeline for expression and purification of protein libraries.

Scientific Applications:

• Drug discovery: Enables exploration of large sequence spaces to identify novel protein candidates relevant to therapeutic discovery.
• Enzyme engineering: Supports design and screening of enzyme variant libraries for activity and specificity optimization.
• Synthetic biology: Facilitates construction of diverse functional protein parts for synthetic biology applications.
• Functional genomics and proteomics: Enables systematic sampling of sequence-function relationships to study protein function and interaction dynamics.

Methodology:

Employs an evolutionary algorithm to design degenerate DNA templates for systematic exploration of protein sequence space, guided by user-defined parameters for composition and diversity.