Problems - Revision history

Frodo: Redirected page to Category:Problems

2014-03-13T03:47:31Z

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	~~This is the general problem page at docking.org. There are also specific problem pages as follows:~~		#REDIRECT [[Category:Problems]]

	* [[DOCK Blaster:Problems]]
	* [[DUD:Problems]]
	* [[DOCK:Problems]]
	* [[ZINC:Problems]]

	~~= Kinds of problems =~~
	~~We differentiate among bugs, blunders, technical problems, algorithmic problems and other problems.~~

	* Blunders are typos or errors that can be put right immediately by typographical correction.
	* Bugs are errors that may be put right, and do not require major new coding, but more than simple typographical correction.
	* Technical problems are ones we know pretty well exactly how to solve, but may require more time or money than we have available, or maybe we are just lazy.
	* Algorithmic problems are cases where the best method of doing something is in some doubt, and requires study. Examples of algorthmic problems are: what is the best way to score a molecule given the constraints of fast docking?
	* There are other problems too. If a problem can be classified as one of the above, that can be helpful.

	~~{{TOCright}}~~

	[[Category:Problems]]

Therese: 21 revisions

2012-10-08T20:31:22Z

21 revisions

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Revision as of 20:31, 8 October 2012

Frodo at 16:10, 7 August 2009

2009-08-07T16:10:21Z

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	* [[ZINC:Problems]]		* [[ZINC:Problems]]

	= ~~Technical Problems~~ =		= Kinds of 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~~.		We differentiate among bugs, blunders, technical problems, algorithmic problems and other problems.

			* Blunders are typos or errors that can be put right immediately by typographical correction.
			* Bugs are errors that may be put right, and do not require major new coding, but more than simple typographical correction.
			* Technical problems are ones we know pretty well exactly how to solve, but may require more time or money than we have available, or maybe we are just lazy.
			* Algorithmic problems are cases where the best method of doing something is in some doubt, and requires study. Examples of algorthmic problems are: what is the best way to score a molecule given the constraints of fast docking?
			* There are other problems too. If a problem can be classified as one of the above, that can be helpful.

	{{TOCright}}		{{TOCright}}






	~~= Philosophical Problems =~~
	*
	*
	*


	[[Category:Problems]]		[[Category:Problems]]

Frodo at 16:02, 7 August 2009

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	~~== 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

	= Philosophical Problems =		= Philosophical Problems =

Frodo at 16:01, 7 August 2009

2009-08-07T16:01:36Z

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	This is the general problem page at docking.org. There are also specific problem pages as follows:		This is the general problem page at docking.org. There are also specific problem pages as follows:


	* [[DOCK Blaster:Problems]]		* [[DOCK Blaster:Problems]]
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	= 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.		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.


	{{TOCright}}		{{TOCright}}





	~~== DUD ==~~
	* more systems
	* get the new paper out
	* new ways of choosing decoys
	* new release

	== DOCK Tools ==		== DOCK Tools ==

Frodo at 16:00, 7 August 2009

2009-08-07T16:00:57Z

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	~~== 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 ==		== DUD ==

Frodo at 16:00, 7 August 2009

2009-08-07T16:00:19Z

← Older revision		Revision as of 16:00, 7 August 2009
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	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.		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
	* yuck out of date.
	* missing molecules

	~~== Known Problems ==~~
	I'm so glad you asked! There are a number of problems we know of, all of which we aim to fix one day. We hope you will agree that the benefits of ZINC as it stands outweigh the problems. Here are a few of the problems we are aware of:

	* Unreasonable tautomers - We generate some tautomers that we shouldn't. Among the ones we know about is CH3-C=NH -> CH2=C-N. Over half (40K+) were removed March 7. More processing to follow in April 2005. (Problem 5/3/7)
	* Aggressive protonation - We generate protonated forms that are probably unreasonable for most targets, such as protonated pyridines. This is an active area of research. Please be patient. (Problem 5/995)
	* Broken flexibase molecules - If you use the flexibase format files, we are aware of a number of broken molecules, including C1S(=O)(=O)CCC1 and molecules with aliphatic rigid fragments. We know about this, and are working to correct it. (Problem 5/996)
	* Corrupt files to download - We offer over 30 million distinct files to download from the ZINC web site. Our quality control is currently such that a few of these are corrupt. If you find one, would you kindly bring it to our attention? We will endeavor to fix it asap. (Problem 5/997)
	* Subsets & Uploads - The subsetting and uploading mechanism is somewhat brittle. We hope to spend time on this soon. (Problem 5/999)
	* Truncated Searches - We currently limit searches to 30 seconds of CPU time, to avoid overwhelming our servers, and to give you at least a partial answer in a timely fashion. We plan to add more servers soon and thereby offer quicker turnaround and more complete answers. Thanks for your patience. (Problem 5/998) [correction: We are at 45 seconds on a trial basis as of Feb 14.]
	* Duplicate backslashes in SMILES files - Fixed 3 March 2005.(Problem 5/1/3)
	* Name of molecule in mol2 file often incorrect. Being fixed currently. Reported by Gandhimathi and Federica Morandi. We consider this an annoying but not a core bug.
	* Ambiguous and syntatically incorrect SMILES for E/Z specification Being fixed currently. Full solution expected in April. (Problem 5/3/10).
	* Wrong annotations - FIXED March 1, 2005. If you find incorrect annotations in files downloaded after March 1, 2005, please write databases at docking.org. (Problem 5/3/1)
	* Wrong molecules in subset - Subsets 1&2 FIXED March 1, 2005. Other subsets being released March 3-5. If you find molecules that do not belong in a subset for files downloaded AFTER March 5, 2005, please write comments at docking.org. (Problem 5/3/2)
	* Wrong charges in mol2 files - The current version of ZINC contains MMFF94 charges rather than AMSOL charges. We regret this error. The workaround is to run mol2 files through a program like molcharge, part of the QuacPac suite from OpenEye. There are many other fine programs that will assign partial atomic charges. The new version of ZINC now in preparation will have AMSOL partial atomic charges.

	~~== Missing Molecules ==~~

	{{TOCright}}		{{TOCright}}

Frodo at 15:59, 7 August 2009

2009-08-07T15:59:40Z

← Older revision		Revision as of 15:59, 7 August 2009
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			This is the general problem page at docking.org. There are also specific problem pages as follows:


			* [[DOCK Blaster:Problems]]
			* [[DUD:Problems]]
			* [[DOCK:Problems]]
			* [[ZINC: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.		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.

Frodo: Current Problems moved to Problems: standardize naming

2009-08-07T15:58:55Z

Current Problems moved to Problems: standardize naming

← Older revision

Revision as of 15:58, 7 August 2009

Frodo: /* ZINC */

2009-02-13T01:14:27Z

ZINC

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 * yuck out of date.
 * missing molecules
 {{TOCright}}