ICDA
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(New page: 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 o...) |
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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'''. | ||
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Quick Start: | Quick Start: | ||
To run ICDA | To run ICDA | ||
| - | + | [[pka]] clust beg end fastpka no adjust yes | |
| - | + | ||
| - | + | ||
To get plop to recognize the altered protonation states, in load pdb .... | To get plop to recognize the altered protonation states, in load pdb .... | ||
| - | + | [[load]] pdb mypdb.pdb pka frompdb [other options] | |
| - | + | ||
Current revision
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]
