Smallworld Databases: Difference between revisions

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== Introduction ==
== Introduction ==
This page will detail the databases on smallworld and arthor.
This page details the databases on Smallworld
 
{{TOCright}}
 
== Smallworld slides/presentations ==
 
https://www.slideshare.net/NextMoveSoftware/smallworld-efficient-maximum-common-substructure-searching-of-large-databases
 
https://www.nextmovesoftware.com/products/SmallWorld.pdf <--- very good, more detailed overview of how the technology works
 
https://www.nextmovesoftware.com/talks/Sayle_InterestingApplicationsOfChemicalGraphEditDistance_ACS_202303.pdf <--- random slides i found not that interesting


== Smallworld Databases ==
== Smallworld Databases ==
Tables of the five smallworld instances running on '''abacus'''.
Tables of the five smallworld instances running on '''abacus'''.
=== sw.docking.org ===
=== sw.docking.org ===
{| class="wikitable"
{| class="wikitable"
|-
|-
! Database !! Description (Always latest version available, shows number when available)
! Database !! Description (Always latest version available, shows number when available)
|-
| BB-All-2020Q2-26.7M.anon || All building blocks in ZINC.
| -
| BB-Now-2020Q2-1.6M.anon || All in-stock building blocks.
|-
| ChemSpace-BB-Stock-Mar2022 || Building blocks sold by ChemSpace from stock.
|-
|-
| ChemSpace-SC-Stock-Mar2022 || Screening compounds sold by ChemSpace.
| ChemSpace-SC-Stock-Mar2022 || Screening compounds sold by ChemSpace.
Line 20: Line 25:
|-
|-
| Informer-Set-22Q3-4M || The ZINC "informer set" (compounds that can be purchased quickly, within a week or so).  
| Informer-Set-22Q3-4M || The ZINC "informer set" (compounds that can be purchased quickly, within a week or so).  
|-
| Mcule-BB-22Q1-2.1M || Building blocks sold by Mcule
|-
|-
| Mcule-22Q1-8.7M || Mcule screening compounds.
| Mcule-22Q1-8.7M || Mcule screening compounds.
Line 48: Line 51:
! Database !! Description (version, number of molecules)
! Database !! Description (version, number of molecules)
|-
|-
| el2_22Q1_290K || Ellman library 2 - isoquinuclidines
| Chembridge On Demand 23Q4 22B
|-
|-
| REAL-Space-22Q1-21B || Enamine private library - password protected.
| Macrocycles Make on Demand 23Q4. 9.9K
|-
|-
| y1-22Q3-57M || Damien Young library #1, substituted piperidines.
| REAL-Space-22Q1-21B || Enamine private library
|-
|-
| zinc22-All || ZINC-22
| zinc22-All || ZINC-22
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|-
|-
| BB-Now-2020Q2-1.6M.anon || ZINC20 Building blocks for rapid delivery (in-stock).  
| BB-Now-2020Q2-1.6M.anon || ZINC20 Building blocks for rapid delivery (in-stock).  
|-
| Mcule stock BB 23Q1  3.5M  || can't be true, but try ordering and let us know
|-
|-
| Mcule-BB-22Q1-2.1M || Mcule building blocks
| Mcule-BB-22Q1-2.1M || Mcule building blocks
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| el2_22Q1_290K || Ellman library 2. isoquinuclidines
| el2_22Q1_290K || Ellman library 2. isoquinuclidines
|-
|-
| Piperazine-22Q3-57M || Damien Young library 1.
| y1-22Q3-57M || Damien Young library #1, substituted piperidines.
|-
|}
|}


== Arthor Databases ==
Tables of the arthor instances.
=== arthor.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| BB-50-22Q1 || ZINC20 Building blocks, best price/delivery-speed combination
|-
| BB-40-22Q1 || ZINC20 building blocks, second tier in stock.
|-
| BB-30-22Q1 || ZINC20 building blocks, third tier in stock
|-
| BB-20-22Q1 || ZINC20 make-on-demand building blocks. Likely  >> $500 . Likely 6 weeks or more.
|-
| BB-10-22Q1 || ZINC20 make-on-demand or expensive building blocks. Like >> $1000. Likely 6 weeks or more.
|-
| BB-ForSale-22Q1 || ZINC20 building blocks (50+40+30+20+10)
|-
| BB-InStock-22Q1 || ZINC20 building blocks (50+40+30)
|-
| ChemSpace-BB-Stock-Mar2022-712K || ChemSpace building blocks
|-
| ChemSpace-SC-Stock-Mar2022-346K || ChemSpace screening compounds
|-
| HMDBMetabolites-20Q1-585 ||  HMDB Metabolites
|-
| In-Stock-19Q4-13.8M || ZINC20 in stock
|-
| Informer-Set-22Q3-4M ||  ZINC20 informer set (fast delivery, modest prices)
|-
| Mcule-22Q1-8.7M || Mcule Screening compounds
|-
| Mcule-V-22Q1-51M ||  Mcule make on demand
|-
| Mcule-BB-22Q1-2.1M || some description
|-
| Mcule-Full-22Q1-60M ||  Mcule SC+BB
|-
| Mcule_ultimate_20Q2-126M || Mcule Ultimate
|-
| REAL-Database-22Q1-00 ||  Enamine REAL one part
|-
| REAL-Database-22Q1-01 || Enamine REAL another part
|-
| TCNMP-20Q1-37K || Traditional Chinese Medicine database
|-
| Wait-OK-19Q4-1.1B || ZINC20 in stock and make on demand
|-
| World-Drugs-20Q1-3K ||  ZINC20 drugs
|-
| WuXi-19Q4-339M || WuXi make-on-demand
|-
| ZINC-All-19Q4-1.4B ||  All ZINC20
|-
| ZINC-Interesting-2019Q4-307K || ZINC20 annotated, bioactive
|-
| ZINC-On-Demand-19Q4-311M ||  ZINC20 make on demand
|-
| ZINC20-ForSale-22Q1 || ZINC20 for sale
|-
|}


=== arthorp.docking.org ===
[[Category:Smallworld]]
{| class="wikitable"
[[Category:Databases]]
|-
[[Category:ZINC]]
! Database !! Description
|-
| el2_22Q1 || some description
|-
| REAL-Space-22Q1-00 ||
|-
| REAL-Space-22Q1-01 || some description
|-
| REAL-Space-22Q1-02 ||
|-
| REAL-Space-22Q1-03 || some description
|-
| REAL-Space-22Q1-04 ||
|-
| REAL-Space-22Q1-05 || some description
|-
| REAL-Space-22Q1-06 ||
|-
| REAL-Space-22Q1-07 || some description
|-
| zinc22-22Q1(H01~H25) ||
|-
|}
=== arthorbb.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| BB-10-22Q1 || some description
|-
| BB-20-22Q1 ||
|-
| BB-30-22Q1 || some description
|-
| BB-40-22Q1 ||
|-
| BB-50-22Q1 || some description
|-
| BB-ForSale-22Q1 ||
|-
| BB-InStock-22Q1 || some description
|-
| ChemSpace-BB-Stock-Mar2022-712K ||
|-
| Mcule-BB-22Q1-2.1M || some description
|-
|}
=== arthorcc.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| el2_22Q1 || some description
|-
|}

Latest revision as of 20:23, 24 May 2024

Introduction

This page details the databases on Smallworld

Smallworld slides/presentations

https://www.slideshare.net/NextMoveSoftware/smallworld-efficient-maximum-common-substructure-searching-of-large-databases

https://www.nextmovesoftware.com/products/SmallWorld.pdf <--- very good, more detailed overview of how the technology works

https://www.nextmovesoftware.com/talks/Sayle_InterestingApplicationsOfChemicalGraphEditDistance_ACS_202303.pdf <--- random slides i found not that interesting

Smallworld Databases

Tables of the five smallworld instances running on abacus.

sw.docking.org

Database Description (Always latest version available, shows number when available)
ChemSpace-SC-Stock-Mar2022 Screening compounds sold by ChemSpace.
In-Stock-2020Q2-13.8M.anon All ZINC in stock compounds.
Informer-Set-22Q3-4M The ZINC "informer set" (compounds that can be purchased quickly, within a week or so).
Mcule-22Q1-8.7M Mcule screening compounds.
Mcule-Full-22Q1-56M Mcule, all compounds
Mcule-V-22Q1-47M Mcule, make-on-demand.
MculeUltimate_20Q2_126M Mcule "Ultimate" library.
REAL-Database-22Q1-4.5B Enamine REAL database. (publicly available)
Wait-OK-2020Q2-1.2B.anon ZINC compounds, in stock combined with make-on-demand.
WuXi-20Q4-2.2B WuXi compounds, almost all make-on-demand.
ZINC-All-2020Q2-1.46B.anon All compounds in ZINC20, including annotated only (not purchasable) compounds.
ZINC-Interesting-2020Q2-300K.anon Drugs, bioactive, natural products, biogenic, or otherwise annotated for activity.

swp.docking.org

Database Description (version, number of molecules)
Chembridge On Demand 23Q4 22B
Macrocycles Make on Demand 23Q4. 9.9K
REAL-Space-22Q1-21B Enamine private library
zinc22-All ZINC-22

swbb.docking.org

Database Description
ChemSpace-BB-Stock-Mar2022 Building blocks for sale from ChemSpace
BB-All-2020Q2-26.7M.anon ZINC20 Building blocks for sale
BB-Now-2020Q2-1.6M.anon ZINC20 Building blocks for rapid delivery (in-stock).
Mcule stock BB 23Q1 3.5M can't be true, but try ordering and let us know
Mcule-BB-22Q1-2.1M Mcule building blocks

swcc.docking.org

Database Description
el2_22Q1_290K Ellman library 2. isoquinuclidines
y1-22Q3-57M Damien Young library #1, substituted piperidines.
Retrieved from "http://wiki.docking.org/index.php?title=Smallworld_Databases&oldid=16046"