RNALYZER – RNA Structural Comparison Framework

RNALYZER

:: DESCRIPTION

RNAlyzer is a computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

RNALYZER

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Java3D
  • OpenGL

:: DOWNLOAD

 RNALYZER

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(12):5978-90. doi: 10.1093/nar/gkt318.
RNAlyzer–novel approach for quality analysis of RNA structural models.
Lukasiak P1, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J.

APoc 1.0 – Large-scale Structural Comparison of Protein Pockets

APoc 1.0

:: DESCRIPTION

APoc (Alignment of Pockets) is a computational method for large-scale structural comparison of protein pockets. A scoring function, Pocket Similarity Score (PS-score), is derived to measure the level of similarity between pockets. Statistical models are employed to estimate the significance of PS-score based on millions of comparisons of random pockets. Apoc is a general, robust method that may be applied to pockets identified by various approaches, such as ligand-binding sites as observed in experimental complex structures, or predicted pockets identified by a pocket detection method. We curate large benchmark data sets to evaluate the performance of APoc and present interesting examples to demonstrate the usefulness of the method.

::DEVELOPER

Center for the Study of Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 APoc

:: MORE INFORMATION

Citation

Bioinformatics (2013) 29 (5): 597-604.
APoc: large-scale identification of similar protein pockets.
Gao M, Skolnick J.