abinitio -- ab initio structure prediction from a sequence with already-prepared fragements and secondary structure prediction.

AnchoredDesign -- Design of a protein-protein interface around a known interaction (the anchor) at the same interface of one partner.

beta_strand_homodimer_design -- Identify exposed (unpaired) beta-strands and design a homodimer using the unpaired strand.

electron_density
1) cryoEM tutorial -- use Rosetta to model structures into cryoEM data.
2) molecular replacement -- use Rosetta to solve difficult molecular replacement problems. 

FlexPepDock_Refinement -- Flexible peptide docking starting from an unrefined model.

fragment_picker -- Prepare fragements for loop modeling or ab initio modeling. Needs a README

ligand_dock -- Docking a ligand into a protein. Separate ligand_setup and ligand_dock demos.

pepspec -- Peptide specificity / flexible backbone design. Designs a peptide to bind around an "anchor" residue on the target protein.

python -- python implementation of relax protocol, to minimize the energy of a structure. Needs a README

rna -- How to prepare an RNA for Rosetta. Needs a README

RNA_Assembly -- Create a model of a large RNA from secondary structure prediction and limited constraint data (e.g. from mutations)

RNA_Denovo -- Predict RNA 3 dimensional structure from sequence.

RNA_Design -- Needs a README to describe scientific goals.

rosetta -- Needs a README. Fragments, pdb, refold and score.

rosetta_scripts -- A number of useful xml scripts

serialization -- Needs a README. Delete or demote?

utility -- Needs a README. Delete or demote?

zipper.sh

### scons setup ###
demo.src.settings
SConscript.demo

### needs a README purgatory ####
fragment_picker -- Prepare fragements for loop modeling or ab initio modeling. Needs a README

### pilot demos -- flagged for deletion ###
rosetta -- DEL
serialization -- DEL
utility -- DEL
abbie -- (pbradley) DEL
andrew -- emailed
chu -- moved to rosetta_source/src/apps/pilot/chu
dan -- DEL
dekim -- DEL
gktaylor -- DEL dekim says DEL, gktaylor says DEL
james -- DEL dekim says DEL (dekim, aleaverfay)
jim -- DEL
lemmongh -- no action, glemmon@gmail.com
liz -- DEL
olli -- emailed oliver
phil -- DEL
sraman -- DEL
vatsan -- DEL
will -- DEL