ICDA

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ICDA (Independent Cluster Decomposition Algorithm) is a computationally efficient method of assigning polar states in proteins. It works by assuming a protein is composed of custers of non-interacting polar residues and combinatorially evaluating all the possibilities within each cluster.

The corresponding plop command for ICDA polar state assignment is pka clust.

Quick Start: To run ICDA

pka clust beg end fastpka no adjust yes

To get plop to recognize the altered protonation states, in load pdb ....

load pdb mypdb.pdb pka frompdb [other options]

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