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RNA folding problem: Is it possible to accurately predict the secondary, tertiary and quaternary structure of a polyribonucleic acid sequence based on its sequence and environment? Protein design : Is it possible to design highly active enzymes de novo for any desired reaction?
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
A plasmid partition system is a mechanism that ensures the stable inheritance of plasmids during bacterial cell division. Each plasmid has its independent replication system which controls the number of copies of the plasmid in a cell.
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. [ 1 ]
The problem of predicting nucleic acid secondary structure is dependent mainly on base pairing and base stacking interactions; many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such ...
Predicting protein tertiary structure from only its amino sequence is a very challenging problem (see protein structure prediction), but using the simpler secondary structure definitions is more tractable. Early methods of secondary-structure prediction were restricted to predicting the three predominate states: helix, sheet, or random coil.
The recognition of long-branch attraction implies that there is some other evidence that suggests that the phylogeny is incorrect. For example, two different sources of data (i.e. molecular and morphological) or even different methods or partition schemes might support different placement for the long-branched groups. [6]
Partition into cliques is the same problem as coloring the complement of the given graph. A related problem is to find a partition that is optimal terms of the number of edges between parts. [3]: GT11, GT12, GT13, GT14, GT15, GT16, ND14 Grundy number of a directed graph. [3]: GT56 Hamiltonian completion [3]: GT34