RRDB

RRDB provides a non-redundant dataset for computational determination of RNA-RNA complex structures to support analysis of noncoding RNA interactions and RNA-RNA docking studies.

Key Features:

• Dataset composition: Contains 123 distinct targets comprising 78 unbound-unbound and 45 bound-unbound (or unbound-bound) test cases.
• Difficulty classification: Classifies targets into three difficulty levels (easy: 47, medium: 38, difficult: 38) based on conformational changes at the interface between bound and unbound structures.
• Bound and unbound cases: Provides both bound and unbound structures for targets to enable assessment of conformational variation in docking.
• Non-redundancy and focus: Assembles a non-redundant dataset tailored for RNA-RNA docking studies and analysis of noncoding RNAs.
• Benchmark testing: Has been tested using ZDOCK 2.1 to characterize docking difficulty and benchmark docking and scoring algorithms.

Scientific Applications:

• Benchmarking: Benchmarking and evaluation of docking and scoring algorithms for RNA-RNA interactions using bound and unbound cases.
• Method development: Development and optimization of computational methods that predict RNA-RNA complex structures.
• Mechanistic studies: Investigation of conformational changes and molecular mechanisms underlying RNA-RNA interactions, including noncoding RNAs.

Methodology:

Targets were compiled and classified into unbound-unbound and bound-unbound (or unbound-bound) cases, categorized by interface conformational changes into easy/medium/difficult levels, and benchmarked using ZDOCK 2.1.