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2025-05-22T17:53:45Z

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	== Are you new here? ==		== Are you new here? ==
	wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, ~~both~~ in academia and in ~~companies~~. We work in five major technology areas:		wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, in academia, non-profits and in pharma and biotech. We work in five major technology areas:
	* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). [[DOCK]]		* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). [[DOCK]]
	* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. [[Smallworld]] and [[Arthor]].		* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. [[Smallworld]] and [[Arthor]].

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2025-05-22T17:52:47Z

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	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and databases may be found via [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology ~~as hosted at the domain "[https://docking.org docking.org]". This wiki~~ serves several [[:Category:Roles \| constituencies]]~~. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic~~. If you are a <b>new member of a lab</b>, please see the [[Welcome group members \| following guide]].		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and databases may be found via [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology, and serves several [[:Category:Roles \| constituencies]]. If you are a <b>new member of a lab</b>, please see the [[Welcome group members \| following guide]]. Docking documentation [https://docs.docking.org docs.docking.org]

	~~Documentation~~ [https://docs.docking.org docs.docking.org]

	=== Relevant Links ===		=== Relevant Links ===

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2025-05-22T17:50:19Z

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	<div id="mainpage"></div><!--		<div id="mainpage"></div><!--
	-->__NOTOC__		-->__NOTOC__
	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and ~~database~~ may be found at [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. If you are a <b>new member of a lab</b>, please see the [[Welcome group members \| following guide]].		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and databases may be found via [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. If you are a <b>new member of a lab</b>, please see the [[Welcome group members \| following guide]].

	Documentation [https://docs.docking.org docs.docking.org]		Documentation [https://docs.docking.org docs.docking.org]

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2025-05-22T17:49:59Z

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	<div id="mainpage"></div><!--		<div id="mainpage"></div><!--
	-->__NOTOC__		-->__NOTOC__
	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and database may be found at [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. ~~lala~~		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and database may be found at [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. If you are a <b>new member of a lab</b>, please see the [[Welcome group members \| following guide]].

	If you are a <b>new member of a lab</b>, please ~~follow~~ the [[Welcome group members \| following guide]].

	Documentation [https://docs.docking.org docs.docking.org]		Documentation [https://docs.docking.org docs.docking.org]

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2025-05-22T17:49:28Z

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← Older revision		Revision as of 17:49, 22 May 2025
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	<div id="mainpage"></div><!--		<div id="mainpage"></div><!--
	-->__NOTOC__		-->__NOTOC__
	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and database may be found at [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala

	If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].		If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].

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2025-05-10T02:43:48Z

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	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "[https://docking.org docking.org]". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala

	If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].		If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].

Sstrizhov at 18:41, 9 May 2025

2025-05-09T18:41:38Z

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	* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]		* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]
	* [[:Category:News \| News]]		* [[:Category:News \| News]]
			* [[Group Meeting \| Group Meeting Times]]
	* [https://x.com/chem4biology/ Outages and Updates]		* [https://x.com/chem4biology/ Outages and Updates]
	* [https://discord.gg/4MpD6UF5AN Chat on Discord]		* [https://discord.gg/4MpD6UF5AN Chat on Discord]

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2025-04-29T18:11:45Z

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	<div id="mainpage"></div><!--		<div id="mainpage"></div><!--
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	Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic.		Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles \| constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala

	If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].		If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].

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2025-04-25T15:59:32Z

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	If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].		If you are a <b>new member of a lab</b>, please follow the [[Welcome group members \| following guide]].

			Documentation [https://docs.docking.org docs.docking.org]

	=== Relevant Links ===		=== Relevant Links ===

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2025-04-05T19:56:59Z

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	== Are you new here? ==		== Are you new here? ==
	wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We work in five major technology areas:		wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We work in five major technology areas:
	* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).		* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). [[DOCK]]
	* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.		* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. [[Smallworld]] and [[Arthor]].
	* 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").		* 3) '''Target prediction'''. Given a molecule, our program [[SEA]] can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").
	* 4) '''Bespoke Chemistry'''. The Chemistry Commons is a platform to help chemists and biologist to collaborate. This system allows chemists to define which molecules their new chemistry can access, and it allows biologists to search through this novel bespoke chemistry.		* 4) '''Bespoke Chemistry'''. The [[Chemistry Commons]] is a platform to help chemists and biologist to collaborate. This system allows chemists to define which molecules their new chemistry can access, and it allows biologists to search through this novel bespoke chemistry.
	* 5) '''Chemical Libraries'''. ZINC is available for download in 2D and 3D.		* 5) '''Chemical Libraries'''. [[ZINC]] is available for download in 2D and 3D.

	We hope you find this website interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.		We hope you find this website interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.