Problems: Difference between revisions
Jump to navigation
Jump to search
(→ZINC) |
No edit summary |
||
| Line 1: | Line 1: | ||
= Technical Problems = | = Technical Problems = | ||
Technical problems can be fixed algorithmically. Scientific problems may also be technical, but what differentiates them is that I cannot describe algorithmically how to solve them. Instead, we should take an experimental approach, probably trying at least two different ways, and seeing which works best. Philosophical problems in this context means that I am not even sure how to phrase a scientific question or a testable hypothesis, but I recognize that there is a problem. | |||
== ZINC == | == ZINC == | ||
* Molecule duplication | * Molecule duplication | ||
| Line 12: | Line 14: | ||
* activity annotations out of date | * activity annotations out of date | ||
* links to supplier web sites sometimes broken | * links to supplier web sites sometimes broken | ||
* documentation | |||
* tutorials | |||
* protocols | |||
* describe the pipeline on-line | |||
* get the new paper out | |||
{{TOCright}} | {{TOCright}} | ||
== DOCK Blaster == | |||
* documentation | |||
* tutorials | |||
* protocols | |||
* get the paper out | |||
== DOCK 6.2 == | |||
* new release | |||
* clean up documentation | |||
== DOCK 3.5.54 == | |||
* prepare new distribution | |||
* documentation | |||
== DUD == | |||
* more systems | |||
* get the new paper out | |||
* new ways of choosing decoys | |||
* new release | |||
== Tools == | |||
* documentation | |||
== Cluster == | == Cluster == | ||
* | * more disk space on line | ||
== DOCK 3.5.54 == | == DOCK 3.5.54 == | ||
Revision as of 21:45, 12 February 2009
Technical Problems
Technical problems can be fixed algorithmically. Scientific problems may also be technical, but what differentiates them is that I cannot describe algorithmically how to solve them. Instead, we should take an experimental approach, probably trying at least two different ways, and seeing which works best. Philosophical problems in this context means that I am not even sure how to phrase a scientific question or a testable hypothesis, but I recognize that there is a problem.
ZINC
- Molecule duplication
- Incorrect representation
- Missing representation
- Out of date catalogs
- Broken molecules
- Probably incorrect enumeration/sampling of stereochemistry both R/S and E/Z
- incorrect treatment of protonation and tautomerization in some cases
- search way too slow
- SEA index out of date
- activity annotations out of date
- links to supplier web sites sometimes broken
- documentation
- tutorials
- protocols
- describe the pipeline on-line
- get the new paper out
DOCK Blaster
- documentation
- tutorials
- protocols
- get the paper out
DOCK 6.2
- new release
- clean up documentation
DOCK 3.5.54
- prepare new distribution
- documentation
DUD
- more systems
- get the new paper out
- new ways of choosing decoys
- new release
Tools
- documentation
Cluster
- more disk space on line
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