RNA 2D structure prediction methods

Single sequence based methods

  • Mfold
  • The mfold web server is one of the oldest web servers in computational molecular biology.

  • RNAfold
  • The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences. Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free energy only predicitions.

  • pKiss
  • pKiss is a tool for folding RNA secondary structures, including two limited classes of pseudoknots.

  • CentroidFold
  • CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. The predicted secondary structure is coloured according to base pairing probabilities.

  • ContextFold
  • Context Fold is an RNA secondary structure prediction tool. It applies feature-rich scoring models, whose parameters were obtained after training on comprehensive datasets.

Multiple sequences based methods

  • CentroidHomfold
  • CentroidHomfold predicts RNA secondary structures by employing automatically collected homologous sequences of the target. Homologous sequences are collected from Rfam using LAST. If homologous sequences are available, CentroidHomfold can predict secondary structures for the target sequence more accurately than CentroidFold using homologous sequence information with the probabilistic consistency transformation for base-pairing probabilities.

  • RNAalifold
  • It will predict a consensus secondary structure of a set of aligned sequences. Current limits are 3000 nt and 300 sequences for an alignment.

RNA Databases

RNA 3D structure databases

  • PDB
  • This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.

  • NDB
  • The NDB contains information about experimentally-determined nucleic acids and complex assemblies. Use the NDB to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids.

RNA sequence and 2D databases

  • Rfam
  • The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).