From CAGT

K2 Submit a Job

K2SA is a protein structure alignment program based on K2. K2SA uses the same basic strategy as K2 but is about 100 times faster. This speed up is the result of

• A fast simulated annealing technique that replaces the genetic algorithm.
• Tighter code.

K2SA alignments should be as good as K2 alignments (or even better!). If you'd like, you can still run the old version of K2.

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PLEASE NOTE: Be sure to use the 'Browse' buttons to locate the PDB files on your computer's hard drive. PDB codes alone will not work - you must have the appropriate files already on your computer to submit to the server.

Protein 1 (PDB file)  
Protein 2 (PDB file)  


impose sequential constraints
do not impose sequential constraints

1000 2000 5000 10000 Maximum number of annealing rounds. (Select a larger number for difficult alignments, a smaller number for easier alignments.)

1 5 10 20 Number of annealing restarts. (Select a larger number for difficult alignments, a smaller number for easier alignments.)

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