International Journal of Molecular Sciences · 2019 · 170 citations · 37 references
Life SciencesBioinformaticsMolecular BiologyComputational BiologyStructural BioinformaticsStructural BiologyNucleic Acid ModelingRna StructurePairwise Residue-residue RestraintsPseudoknot PredictionResidue-residue InteractionsRna Structural ModelingRna Structure DeterminationRna Structure PredictionStructure-function Relationships In RnaWeb Server Architecture
3D structures of RNAs are the basis for understanding their biological functions. However, experimentally solved RNA 3D structures are very limited in comparison with known RNA sequences up to now. Therefore, many computational methods have been proposed to solve this problem, including our 3dRNA. In recent years, 3dRNA has been greatly improved by adding several important features, including structure sampling, structure ranking and structure optimization under residue-residue restraints. Particularly, the optimization procedure with restraints enables 3dRNA to treat pseudoknots in a new way. These new features of 3dRNA can greatly promote its performance and have been integrated into the 3dRNA v2.0 web server. Here we introduce these new features in the 3dRNA v2.0 web server for the users.
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The Amber biomolecular simulation programs
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Infernal 1.1: 100-fold faster RNA homology searches
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