PFP - Protein fingerprint generation - calculates a novel fingerprint for proteins and, optionally, compares the fingerprints of two proteins for best match - standalone.
RNA tool - RNAComposer - Automated 3D structure composition for large RNAs - online.RNA tool - ModeRNA server - A server for RNA structure modeling and analysis - online.RNA tool - iFoldRNA - three-dimensional RNA structure prediction and folding - online.RNAMoIP - Towards 3D structure prediction of large RNA molecules - an integer programming framework to insert local 3D motifs in RNA secondary structure - standalone.RNA tool - RSIM, an improved RNA fragment assembly method - online.RNA tool - The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data - online.RNA tool - IPknot - fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming - online.RNA tool - CentroidFold Web application - online.RNA tool - CentroidHomfold-LAST - accurate prediction of RNA secondary structure using automatically collected homologous sequences - online.CompaRNA - A server for continuous benchmarking of automated methods for RNA secondary structure prediction - online.PETfold - The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences - online.MicroRNA - MicroRNA discovery by similarity search to a database of RNA-seq profiles - database.miRClassify - An advanced web server for miRNA family classification and annotation - online.Modorama - MODexplorer an integrated tool for exploring protein sequence, structure and function relationships (2013) and MODalign (a rich target-template alignment editor 2012) - online.iceLogo - The iceLogo web server and SOAP service for determining protein consensus sequences - online.InteractiveROSETTA - A graphical user interface for the PyRosetta protein modeling suitee - standalone.RBO Aleph - The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone.LYRA - A webserver for lymphocyte receptor structural modeling - online.RNA-Redesign - A web server for fixed-backbone 3D design of RNA - online.R3D-2-MSA - R3D-2-MSA - the RNA 3D structure-to-multiple sequence alignment server - online.RNAssess - A web server for quality assessment of RNA 3D structures - online.RosettaMP - An Integrated Framework Advancing Membrane Protein Modeling and Design - online.GPCRserver - An accurate and novel G protein-coupled receptor predictor - online.FoldNucleus - Web server for the prediction of RNA and protein folding nuclei from their 3D structures - online.NPDock - A web server for protein nucleic acid docking - online.- A high-throughput protein structure prediction server based on remote homologue recognition - online.GPCR-ModSim - A web based solution for modeling G-protein coupled receptors (includes a membrane insertion and molecular dynamics (MD) equilibration protocol) - online.CoinFold - Protein contact prediction and contact-assisted protein folding (input sequence) - online.
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