FoldNucleus

FoldNucleus identifies folding nuclei in RNA and protein three-dimensional structures to analyze the rate-limiting structural elements that constrain folding kinetics.

Key Features:

• Broad Applicability: Supports analysis of RNAs with known 3D structures, including pseudoknots, transfer RNAs (tRNAs), hairpins, and ribozymes, and of proteins with known 3D structures smaller than 200 amino acid residues.
• Folding Nucleus Calculation: Calculates the folding nucleus, defined as the minimal set of structural elements that must form for efficient folding of the biopolymer.
• Comparative Ф (phi) Analysis: Enables comparison between calculated and experimentally determined Ф (phi) values to identify residues or structural elements that are critical for folding rates.

Scientific Applications:

• RNA Folding Studies: Identification of folding nuclei in diverse RNA structures to elucidate pathways and constraints of rapid RNA folding.
• Protein Folding Research: Determination of rate-limiting structural elements for proteins smaller than 200 amino acids to inform studies of stability and folding mechanisms.
• Comparative Kinetics Analysis: Comparison of calculated and experimental Ф (phi) values to refine models of folding kinetics and to generate hypotheses about rate-limiting steps.

Methodology:

Employs computational algorithms to analyze known 3D structures of RNA and proteins and determine which structural elements constitute the folding nucleus, grounded in principles of molecular kinetics and structural biology.