Smallworld and Arthor 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 and Arthor.
 
{{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
! Database !! Description (Always latest version available, shows number when available)
|-
|-
| BB-All-2020Q2-26.7M.anon || some description
| BB-All-2020Q2-26.7M.anon || All building blocks in ZINC.
|-
|-
| BB-Now-2020Q2-1.6M.anon ||  
| BB-Now-2020Q2-1.6M.anon || All in-stock building blocks.
|-
|-
| ChemSpace-BB-Stock-Mar2022 ||
| ChemSpace-BB-Stock-Mar2022 || Building blocks sold by ChemSpace from stock.
|-
|-
| ChemSpace-SC-Stock-Mar2022 ||
| ChemSpace-SC-Stock-Mar2022 || Screening compounds sold by ChemSpace.
|-
|-
| In-Stock-2020Q2-13.8M.anon ||  
| In-Stock-2020Q2-13.8M.anon || All ZINC in stock compounds.
|-
|-
| Informer-Set-22Q3-4M ||
| Informer-Set-22Q3-4M || The ZINC "informer set" (compounds that can be purchased quickly, within a week or so).
|-
|-
| Mcule-BB-22Q1-2.1M ||
| Mcule-BB-22Q1-2.1M || Building blocks sold by Mcule
|-
|-
| Mcule-22Q1-8.7M ||
| Mcule-22Q1-8.7M || Mcule screening compounds.
|-
|-
| Mcule-Full-22Q1-56M ||
| Mcule-Full-22Q1-56M || Mcule, all compounds
|-
|-
| Mcule-V-22Q1-47M ||
| Mcule-V-22Q1-47M || Mcule, make-on-demand.
|-
|-
| MculeUltimate_20Q2_126M ||
| MculeUltimate_20Q2_126M || Mcule "Ultimate" library.
|-
|-
| REAL-Database-22Q1-4.5B ||
| REAL-Database-22Q1-4.5B || Enamine REAL database. (publicly available)
|-
|-
| Wait-OK-2020Q2-1.2B.anon ||
| Wait-OK-2020Q2-1.2B.anon || ZINC compounds, in stock combined with make-on-demand.
|-
|-
| WuXi-20Q4-2.2B ||
| WuXi-20Q4-2.2B || WuXi compounds, almost all make-on-demand.
|-
|-
| ZINC-All-2020Q2-1.46B.anon ||
| ZINC-All-2020Q2-1.46B.anon || All compounds in ZINC20, including annotated only (not purchasable) compounds.
|-
|-
| ZINC-Interesting-2020Q2-300K.anon ||
| ZINC-Interesting-2020Q2-300K.anon || Drugs, bioactive, natural products, biogenic, or otherwise annotated for activity.
|-
|-
|}
|}
=== swp.docking.org ===
=== swp.docking.org ===
{| class="wikitable"
{| class="wikitable"
|-
|-
! Database !! Description
! Database !! Description (version, number of molecules)
|-
|-
| el2_22Q1_290K || some description
| el2_22Q1_290K || Ellman library 2 - isoquinuclidines
|-
|-
| REAL-Space-22Q1-21B ||
| REAL-Space-22Q1-21B || Enamine private library - password protected.
|-
|-
| y1-22Q3-57M ||  
| y1-22Q3-57M || Damien Young library #1, substituted piperidines.
|-
|-
| zinc22-All ||
| zinc22-All || ZINC-22
|-
|}
=== swc.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| REAL-UCSF-21Q4-18.5B || some description
|-
|-
|}
|}
=== swbb.docking.org ===
=== swbb.docking.org ===
{| class="wikitable"
{| class="wikitable"
Line 69: Line 74:
! Database !! Description
! Database !! Description
|-
|-
| ChemSpace-BB-Stock-Mar2022 || some description
| ChemSpace-BB-Stock-Mar2022 || Building blocks for sale from ChemSpace
|-
|-
| BB-All-2020Q2-26.7M.anon ||
| BB-All-2020Q2-26.7M.anon || ZINC20 Building blocks for sale
|-
|-
| BB-Now-2020Q2-1.6M.anon ||  
| BB-Now-2020Q2-1.6M.anon || ZINC20 Building blocks for rapid delivery (in-stock).
|-
|-
| Mcule-BB-22Q1-2.1M ||
| Mcule-BB-22Q1-2.1M || Mcule building blocks
|-
|-
|}
|}
=== swcc.docking.org ===
=== swcc.docking.org ===
{| class="wikitable"
{| class="wikitable"
Line 83: Line 89:
! Database !! Description
! Database !! Description
|-
|-
| el2_22Q1_290K || some description
| el2_22Q1_290K || Ellman library 2. isoquinuclidines
|-
|-
| Piperazine-22Q3-57M ||
| Piperazine-22Q3-57M || Damien Young library 1.
|-
|-
|}
|}
== Arthor Databases ==
== Arthor Databases ==
Tables of the arthor instances.
Tables of the arthor instances.
Line 95: Line 102:
! Database !! Description
! Database !! Description
|-
|-
| BB-10-22Q1 || some description
| BB-50-22Q1 || ZINC20 Building blocks, best price/delivery-speed combination
|-
|-
| BB-20-22Q1 ||  
| BB-40-22Q1 || ZINC20 building blocks, second tier in stock.
|-
|-
| BB-30-22Q1 || some description
| BB-30-22Q1 || ZINC20 building blocks, third tier in stock
|-
|-
| BB-40-22Q1 ||  
| BB-20-22Q1 || ZINC20 make-on-demand building blocks. Likely  >> $500 . Likely 6 weeks or more.
|-
|-
| BB-50-22Q1 || some description
| BB-10-22Q1 || ZINC20 make-on-demand or expensive building blocks. Like >> $1000. Likely 6 weeks or more.
|-
|-
| BB-ForSale-22Q1 ||  
| BB-ForSale-22Q1 || ZINC20 building blocks (50+40+30+20+10)
|-
|-
| BB-InStock-22Q1 || some description
| BB-InStock-22Q1 || ZINC20 building blocks (50+40+30)
|-
|-
| ChemSpace-BB-Stock-Mar2022-712K ||  
| ChemSpace-BB-Stock-Mar2022-712K || ChemSpace building blocks
|-
|-
| ChemSpace-SC-Stock-Mar2022-346K || some description
| ChemSpace-SC-Stock-Mar2022-346K || ChemSpace screening compounds
|-
|-
| HMDBMetabolites-20Q1-585 ||  
| HMDBMetabolites-20Q1-585 || HMDB Metabolites
|-
|-
| In-Stock-19Q4-13.8M || some description
| In-Stock-19Q4-13.8M || ZINC20 in stock
|-
|-
| Informer-Set-22Q3-4M ||   
| Informer-Set-22Q3-4M ||  ZINC20 informer set (fast delivery, modest prices)
|-
|-
| Mcule-22Q1-8.7M || some description
| Mcule-22Q1-8.7M || Mcule Screening compounds
|-
|-
| Mcule-V-22Q1-51M ||   
| Mcule-V-22Q1-51M ||  Mcule make on demand
|-
|-
| Mcule-BB-22Q1-2.1M || some description  
| Mcule-BB-22Q1-2.1M || some description  
|-
|-
| Mcule-Full-22Q1-60M ||   
| Mcule-Full-22Q1-60M ||  Mcule SC+BB
|-
|-
| Mcule_ultimate_20Q2-126M || some description
| Mcule_ultimate_20Q2-126M || Mcule Ultimate
|-
|-
| REAL-Database-22Q1-00 ||   
| REAL-Database-22Q1-00 ||  Enamine REAL one part
|-
|-
| REAL-Database-22Q1-01 || some description
| REAL-Database-22Q1-01 || Enamine REAL another part
|-
|-
| TCNMP-20Q1-37K ||  
| TCNMP-20Q1-37K || Traditional Chinese Medicine database
|-
|-
| Wait-OK-19Q4-1.1B || some description
| Wait-OK-19Q4-1.1B || ZINC20 in stock and make on demand
|-
|-
| World-Drugs-20Q1-3K ||  
| World-Drugs-20Q1-3K || ZINC20 drugs
|-
|-
| WuXi-19Q4-339M || some description
| WuXi-19Q4-339M || WuXi make-on-demand
|-
|-
| ZINC-All-19Q4-1.4B ||   
| ZINC-All-19Q4-1.4B ||  All ZINC20
|-
|-
| ZINC-Interesting-2019Q4-307K || some description
| ZINC-Interesting-2019Q4-307K || ZINC20 annotated, bioactive
|-
|-
| ZINC-On-Demand-19Q4-311M ||   
| ZINC-On-Demand-19Q4-311M ||  ZINC20 make on demand
|-
|-
| ZINC20-ForSale-22Q1 || some description
| ZINC20-ForSale-22Q1 || ZINC20 for sale
|-
|-
|}
|}
=== arthorp.docking.org ===
=== arthorp.docking.org ===
{| class="wikitable"
{| class="wikitable"
Line 174: Line 182:
|-
|-
| zinc22-22Q1(H01~H25) ||  
| zinc22-22Q1(H01~H25) ||  
|-
|}
=== arthorc.docking.org ===
{| class="wikitable"
|-
! Database !! Description
|-
| REAL_UCSF_21Q4_S || some description
|-
| REAL_UCSF_21Q4_M(H15~H25) ||
|-
| REAL_UCSF_21Q4_M(H26~H29) || some description
|-
| REAL_UCSF_21Q4_M(H30~H35) ||
|-
|-
|}
|}

Latest revision as of 19:27, 13 June 2023

Introduction

This page details the databases on Smallworld and Arthor.

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)
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.
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-BB-22Q1-2.1M Building blocks sold by Mcule
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)
el2_22Q1_290K Ellman library 2 - isoquinuclidines
REAL-Space-22Q1-21B Enamine private library - password protected.
y1-22Q3-57M Damien Young library #1, substituted piperidines.
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-BB-22Q1-2.1M Mcule building blocks

swcc.docking.org

Database Description
el2_22Q1_290K Ellman library 2. isoquinuclidines
Piperazine-22Q3-57M Damien Young library 1.

Arthor Databases

Tables of the arthor instances.

arthor.docking.org

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

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

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

Database Description
el2_22Q1 some description
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