SPRINT: side-chain prediction inference toolbox for multistate protein design.
SPRINT is a software package that performs computational multistate protein design using state-of-the-art inference on probabilistic graphical models. The input to SPRINT is a list of protein structures, the rotamers modeled for each structure and the pre-calculated rotamer energies. Probabilistic inference is performed using the belief propagation or A* algorithms, and dead-end elimination can be applied as pre-processing. The output can either be a list of amino acid sequences simultaneously compatible with these structures, or probabilistic amino acid profiles compatible with the structures. In addition, higher order (e.g. pairwise) amino acid probabilities can also be predicted. Finally, SPRINT also has a module for protein side-chain prediction and single-state design.


BACKGROUND
The full C++ source code for SPRINT can be freely downloaded from http://www.protonet.cs.huji.ac.il/sprint.
Fromer
Menachem
M
School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel. fromer@cs.huji.ac.il
Yanover
Chen
C
Harel
Amir
A
Shachar
Ori
O
Weiss
Yair
Y
Linial
Michal
M
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D015233:Models, Statistical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D000596:Amino Acids; D011506:Proteins