NeededPFold

NeededPFold is a software tool for RNA secondary structure prediction and design. It combines energy-based folding with probabilistic sampling and integrates experimental constraints and phylogenetic information to improve accuracy.

It extends traditional folding algorithms by allowing constraint-based specification of required base pairs or forbidden interactions, and by incorporating chemical probing data such as SHAPE reactivities as soft constraints. It uses a dynamic programming core for base-pair probabilities and can generate suboptimal structures along with a partition function, providing confidence estimates for predicted base pairs. It supports analysis of long RNAs and modular motifs.

NeededPFold is open-source and hosted on GitHub. It is implemented in Python and C, with a command-line interface and a web-based frontend. It accepts FASTA sequences and optional alignment input, constraints, and probing data, and outputs dot-bracket structures, pairing probabilities, and energy landscapes. It is designed for researchers in molecular biology, bioinformatics, and education.

Development aimed to address limitations of existing tools in integrating multiple data types. It has been cited in early demonstrations and is part of ongoing efforts to improve RNA structure-aware design. Future work includes improving scalability and integrating experimental feedback loops.