RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

Abstract

Summary: Co-crystallization experiments of proteins with nucleic acids do not guarantee that both components are present in the crystal. We have previously developed DIBER to predict crystal content when protein and DNA are present in the crystallization mix. Here, we present RIBER, which should be used when protein and RNA are in the crystallization drop. The combined RIBER/DIBER suite builds on machine learning techniques to make reliable, quantitative predictions of crystal content for non-expert users and high throughput crystallography. Availability and Implementation: The program source code, Linux binaries and a webserver are available at http://diber.iimcb.gov.pl/. RIBER/DIBER requires diffraction data to at least 3.0 Å resolution in MTZ or CIF (webserver only) format. The program is written in C/C++ and relies on the CCP4 (Winn, et al., 2011) and Clipper (Cowtan, 2003) libraries for handling diffraction data. The LIBSVM (Chang and Lin, 2011) library is used for decision making. The RIBER/DIBER code is subject to the GNU Public License.