NNDB

NNDB provides curated nearest-neighbor thermodynamic parameter sets and descriptive rules for predicting nucleic acid secondary structure stabilities, supporting calculations of RNA folding free energy and enthalpy.

Key Features:

• Parameter Sets: Comprehensive nearest-neighbor thermodynamic parameter sets for nucleic acid secondary structure stability prediction.
• Descriptive Rules and Texts: Detailed rules and explanatory text that define how parameters apply to specific secondary-structure motifs.
• Sequence-Dependent Parameters: Sequence-dependent parameter tables provided in plain text and HTML formats.
• Literature References: References to the experimental literature that support and document each parameter set.

Scientific Applications:

• RNA Folding Thermodynamics: Calculation of RNA folding free energy and enthalpy changes using nearest-neighbor parameters.
• RNA Secondary Structure Prediction: Parameter-based modeling of RNA secondary structures to inform structure–function analyses.
• Parameter Validation and Traceability: Tracing the empirical basis of parameter values to primary experimental literature for reproducibility and validation.

Methodology:

Collection and organization of experimentally derived nearest-neighbor parameters with structured presentation of descriptive rules and sequence-dependent parameter tables in text and HTML formats.