1. Background RNA secondary structure Pseudoknots Non-coding RNA 2. CONTRAfold: Probabilistic RNA folding Overview of the algorithm Details of the algorithm Performance of CONTRAfold 3. Other RNA folding methods: Physics-based models and Stochastic Context Free Grammars Physics-based models Stochastic Context Free Grammars Advantages of CONTRAfold over these other approaches 4. How RNA folding ...

JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service ...

During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorga...

Accurately aligning distant protein sequences is notoriously difficult. Since the amino acid sequence alone often does not provide enough information to obtain accurate alignments under the standard alignment scoring functions, a recent approach to improving alignment accuracy is to use additional information such as secondary structure. We make several advances in alignment of protein sequence...

It has become clear recently that there are many RNAs that are not translated into proteins, instead they work as functional molecules. These RNAs are called “non-coding RNAs.” Predicting the secondary structure of these RNAs is important for understanding their functions. We will therefore focus on Nussinov’s algorithm and the SCFG version of Nussinov’s algorithm as useful techniques for predi...

Algorithms for prediction of RNA secondary structure— the set of base pairsthat form when an RNA molecule folds— are valuable to biologists who aim tounderstand RNA structure and function. Improving the accuracy and efficiencyof prediction methods is an ongoing challenge, particularly for pseudoknottedsecondary structures, in which base pairs overlap. This challenge is biologica...

A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the m...

The combination of classifiers has been proposed as a method to improve the accuracy achieved by a single classifier. In this study, the performances of optimistic and pessimistic ordered weighted averaging operators for protein secondary structure classifiers fusion have been investigated. Each secondary structure classifier outputs a unique structure for each input residue. We used confusion ...