Rclick: a web server for comparison of RNA 3D structures.
RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures.
Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
Minh N
MN
Nguyen
Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore Biomolecular Modeling and Design Division, Singapore 138671 Singapore, Department of Biological Sciences, National University of Singapore, Singapore and School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
Chandra
C
Verma
D000595:Amino Acid Sequence; D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
D016601:RNA-Binding Proteins; D012313:RNA