ICDA

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'''ICDA''' ('''Independent Cluster Decomposition Algorithm''') is a [[pka]] [[Plop Commands|command]] used to assign protonation states.
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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.
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The corresponding [[plop command]] for ICDA polar state assignment is '''pka clust'''.
Quick Start:
Quick Start:
To run ICDA
To run ICDA
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<big>
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[[pka]] clust beg end fastpka no adjust yes
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pka clust beg end fastpka no adjust yes
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</big>
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To get plop to recognize the altered protonation states, in load pdb ....
To get plop to recognize the altered protonation states, in load pdb ....
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<big>
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[[load]] pdb mypdb.pdb pka frompdb [other options]
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load pdb mypdb.pdb pka frompdb [other options]
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</big>
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<references/>

Revision as of 03:30, 29 January 2012

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]

<references/>

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