XYZ4D is a NMRspy extension written in JAVA to assist the assignment of backbone resonances of large proteins without the use of deuterium and specific labeling. It is based on a strategy recently developed in our lab, which extends the size limit for structure determination by NMR spectroscopy to 42 kDa for monomeric proteins and to 65 kDa for differentially labeled multimeric proteins.
SCAssign (side-chain assignment) is a Sparky extension written in Python to assist the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labled large proteins. It is based on a general strategy recently developed in our lab that makes use of 4D 13C,15N-edited NOESY, MQ-(H)CCmHm-TOCSY, and prior backbone assignments. The program runs on all operating systems for which Sparky is available, and is easy to install, setup and use. Not only can it accelerate the assignment process, it also allows assignments from weak NOEs, which used to be infeasible with manual approach.
STARS is a graphics package for doing statistics on inter-atomic distances and torsion angles in protein secondary structures from a protein crystal structure database. It allows one to obtain both the graphical view and text format of distributions of the distances and angles for atoms located in 10 types of protein secondary structures.
MPGA is a script written in Python to search for optimal ensemble from pre-generated structure pool, especially for large intrinsically disordered proteins. It is a mixed algorithm of matching pursuit and genetic algorithm, which takes advantages both from matching pursuit to reduce the search space and from genetic algorithm to free the requirement on the constraint types for structure determination.