Jun Li1, Sicheng Zhang1, Dong Zhang2, Shi-Jie Chen1. 1. Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri, 65211, USA. 2. College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, China.
Abstract
SUMMARY: RNA 3D structures are critical for understanding their functions and for RNA-targeted drug design. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. Therefore, the computer-aided structure prediction of RNA 3D structures from sequences becomes a highly desirable solution to this problem. Here, we present a pipeline server for RNA 3D structure prediction from sequences that integrates the Vfold2D, Vfold3D, and VfoldLA programs. The Vfold2D program can incorporate the SHAPE experimental data in 2D structure prediction. The pipeline can also automatically extract 2D structural constraints from the Rfam database. Furthermore, with a significantly expanded 3D template database for various motifs, this Vfold-Pipeline server can efficiently return accurate 3D structure predictions or reliable initial 3D structures for further refinement. AVAILABILITY AND IMPLEMENTATION: http://rna.physics.missouri.edu/vfoldPipeline/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: RNA 3D structures are critical for understanding their functions and for RNA-targeted drug design. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. Therefore, the computer-aided structure prediction of RNA 3D structures from sequences becomes a highly desirable solution to this problem. Here, we present a pipeline server for RNA 3D structure prediction from sequences that integrates the Vfold2D, Vfold3D, and VfoldLA programs. The Vfold2D program can incorporate the SHAPE experimental data in 2D structure prediction. The pipeline can also automatically extract 2D structural constraints from the Rfam database. Furthermore, with a significantly expanded 3D template database for various motifs, this Vfold-Pipeline server can efficiently return accurate 3D structure predictions or reliable initial 3D structures for further refinement. AVAILABILITY AND IMPLEMENTATION: http://rna.physics.missouri.edu/vfoldPipeline/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Mariusz Popenda; Marta Szachniuk; Maciej Antczak; Katarzyna J Purzycka; Piotr Lukasiak; Natalia Bartol; Jacek Blazewicz; Ryszard W Adamiak Journal: Nucleic Acids Res Date: 2012-04-26 Impact factor: 16.971