Problems: Difference between revisions
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= Technical Problems = | |||
== ZINC == | |||
** some molecules are duplicated | ** some molecules are duplicated | ||
** treatment of protonation and tautomerization is unsatisfactory | ** treatment of protonation and tautomerization is unsatisfactory | ||
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{{TOCright}} | {{TOCright}} | ||
== Cluster == | |||
** it is too easy to overload | ** it is too easy to overload | ||
** Offspring's backplane has issues | ** Offspring's backplane has issues | ||
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** | ** | ||
== DOCK 3.5.54 == | |||
** collisions | ** collisions | ||
** out of box detection | ** out of box detection | ||
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** | ** | ||
== DOCK 6 == | |||
** | ** | ||
** | ** | ||
| Line 28: | Line 28: | ||
** | ** | ||
= Scientific Problems = | |||
== Docking == | |||
** treatment of entropy | ** treatment of entropy | ||
** treatment of desolvation | ** treatment of desolvation | ||
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** ligand internal energy | ** ligand internal energy | ||
= Philosophical Problems = | |||
* | * | ||
* | * | ||
Revision as of 19:59, 12 February 2009
Technical Problems
ZINC
- some molecules are duplicated
- treatment of protonation and tautomerization is unsatisfactory
- treatment of E/Z isomerism is unsatisfactory
Cluster
- it is too easy to overload
- Offspring's backplane has issues
- Node O/S update - Michael has ideas
- bjork needs to be rebuilt
- garbage still needs a 4->5 upgrade
- switch in 508 not correctly negotiating with workstations
DOCK 3.5.54
- collisions
- out of box detection
- ligand internal energy
DOCK 6
Scientific Problems
Docking
- treatment of entropy
- treatment of desolvation
- treatment of induced-fit effects
- ligand internal energy