Research projects

MC-Sym: Three-dimensional molecular modeling using constraint satisfaction.

Mc-Sym is a software that builds RNA 3-D structures using coordinates and relations between residues extracted from X-ray crystallography and NMR found in the RCSB Protein Data Bank and the Rutgers Nucleic Acid Database and from theoretical models. Constraints can be applied to the building procedure to ensure that the generated models are valid. The RNA structures properties and constraints are entered in a script or interactively within the mcsym interpreter.

Annotator: RNA secondary structure annotation.

The simple Mc-Annotate program analyzes a RNA structure and identifies the following components of the structure: sequences, residue conformations, base-pairs, structural elements that interact, base triples, adjacent interactions (stacked, paired or not), non-adjacent stacked interactions, helices (bulges of length 2 or less), strands (single-strands, loops, hairpins, bulges) and pseudoknots.

Base pair classification

Rnaml: A standard syntax for exchanging RNA information.

This is the main resources page for the RNAML syntax for exchanging RNA information. This syntax was designed to easily express data on RNA sequence and structure, and to allow the transmission of information among the RNA community.

SPF: A finder of structurally significant regions in RNA sequences.

Our structural pattern finder is a tool that identify regions of a given RNA or DNA sequence that possess a high probability of being structured. This is achieved by computing, for each region, the difference between the folding free energy of the native sequence with the average folding free energy of randomized sequences of the same base composition.