Problems: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
= Technical Problems = | = Technical Problems = | ||
Technical problems | Technical problems are ones where we think we know pretty well exactly how to solve them, algorithmically. Scientific problems may be technical, but are differentiated because 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 == | ||
| Line 14: | 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* activity annotations out of date | * activity annotations out of date | ||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 | ||
* tutorials | * tutorials | ||
* protocols | * protocols | ||
| Line 23: | Line 22: | ||
== DOCK Blaster == | == DOCK Blaster == | ||
* tutorials | * tutorials | ||
* protocols | * protocols | ||
| Line 30: | Line 28: | ||
== DOCK 6.2 == | == DOCK 6.2 == | ||
* new release | * new release | ||
* | * documentation | ||
== DOCK 3.5.54 == | == DOCK 3.5.54 == | ||
* prepare new distribution | * prepare new distribution | ||
* "collisions" | * "collisions" | ||
* inline out of box detection | * inline out of box detection | ||
Revision as of 00:42, 13 February 2009
Technical Problems
Technical problems are ones where we think we know pretty well exactly how to solve them, algorithmically. Scientific problems may be technical, but are differentiated because 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- Out of date catalogs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- SEA index out of date
- activity annotations out of date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
- tutorials
- protocols
- describe the pipeline on-line
- get the new paper out
DOCK Blaster
- tutorials
- protocols
- get the paper out
DOCK 6.2
- new release
- documentation
DOCK 3.5.54
- prepare new distribution
- "collisions"
- inline out of box detection
- ligand internal energy
- write out multiple structures for PLOP
DUD
- more systems
- get the new paper out
- new ways of choosing decoys
- new release
DOCK Tools
- documentation
Infrastructure
- more disk space on line
Scientific Problems
Docking
- treatment of entropy
- treatment of receptor desolvation
- treatment of induced-fit effects
- ligand internal energy