ACD/LogS0 GALAS - Revision history

Kirilas at 10:11, 15 June 2017

2017-06-15T10:11:15Z

← Older revision		Revision as of 10:11, 15 June 2017
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	==Technical information==		==Technical information==

Kirilas: /* Technical information */

2013-03-20T11:09:55Z

Technical information

← Older revision		Revision as of 11:09, 20 March 2013
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	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	~~Aqueous solubility~~ module provides the quantitative estimate of the compound’s solubility in water at 25°C (in terms of intrinsic solubility Log S<sub>0</sub>, mmol/ml) ~~using a fragmental~~ GALAS (~~<b>G<~~/~~b>lobal, <b>A<~~/~~b>djusted <b>L<~~/~~b>ocally~~ <b>A</b>~~ccording~~ to <b>S</b>~~imilarity)~~ model. ~~The latter methodology allows the module~~ to ~~provide~~ a ~~quantitative assessment~~ of the ~~quality~~ of ~~each prediction in~~ the ~~form of Reliability Index value~~.
			===Description of ACD/LogS0 GALAS Algorithm===

			ACD/LogS0 GALAS module provides provides the quantitative estimate of the compound’s solubility in water at 25°C (in terms of intrinsic solubility Log S<sub>0</sub>, mmol/ml) derived on the basis of GALAS (Global, Adjusted Locally According to Similarity) modeling methodology (please refer to [http://www.ncbi.nlm.nih.gov/pubmed/20373217] for more details).

			Each GALAS model consists of two parts:
			* Global (baseline) statistical model that reflects general trends in the variation of the property of interest.
			* Similarity-based routine that performs local correction of baseline predictions taking into account the differences between baseline and experimental log''S''<sub>0</sub> values for the most similar training set compounds.

			GALAS methodology also provides the basis for estimating reliability of predictions by the means of calculated Reliability Index (''RI'') value that takes into account:
			* Similarity of tested compound to the training set molecules.
			* Consistence of experimental log''S''<sub>0</sub> values and baseline model prediction for the most similar similar compounds from the training set.

			Reliability Index ranges from 0 to 1 (0 corresponds to a completely unreliable, and 1 - a highly reliable prediction) and serves as an indication whether a submitted compound falls within the Model Applicability Domain. Compounds obtaining predictions ''RI'' < 0.3 are considered outside of the Applicability Domain of the model.

			===Experimental Data===

	'''Training set size:''' 4,764<br>		'''Training set size:''' 4,764<br>
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	<nowiki>*</nowiki> - Articles reporting the models of solubility in pure water (LogS<sub>w</sub>) by other authors were the predominant type among analyzed literature, meaning that each publication contained larger collections of experimental data (usually in the order of tens or hundreds compounds) compiled from corresponding original experimental articles. Original LogS<sub>w</sub> data had been converted to LogS<sub>0</sub> prior to modeling.		<nowiki>*</nowiki> - Articles reporting the models of solubility in pure water (LogS<sub>w</sub>) by other authors were the predominant type among analyzed literature, meaning that each publication contained larger collections of experimental data (usually in the order of tens or hundreds compounds) compiled from corresponding original experimental articles. Original LogS<sub>w</sub> data had been converted to LogS<sub>0</sub> prior to modeling.
	</span>		</span>
	~~<br>~~
	====Internal Validation====		===Internal Validation===
	~~<br>~~
	{\| cellpadding="2" cellspacing="0" style="border-top:2px solid black; border-bottom:2px solid black"		{\| cellpadding="2" cellspacing="0" style="border-top:2px solid black; border-bottom:2px solid black"
	\|+ <b>Table 1.</b> ACD/LogS<sub>0</sub> model performance statistics for various fractions of the internal validation set.		\|+ <b>Table 1.</b> ACD/LogS<sub>0</sub> model performance statistics for various fractions of the internal validation set.

Kirilas: /* Technical information */

2013-01-22T09:35:03Z

Technical information

← Older revision		Revision as of 09:35, 22 January 2013
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	<div class="mw-collapsible-content">		<div class="mw-collapsible-content">
	Aqueous solubility module provides the quantitative estimate of the compound’s solubility (Log S<sub>w</sub>, mmol~~/ml and S<sub>w</sub> mg~~/ml) ~~in pure water at 25°C~~ using a fragmental GALAS (<b>G</b>lobal, <b>A</b>djusted <b>L</b>ocally <b>A</b>ccording to <b>S</b>imilarity) model. The latter methodology allows the module to provide a quantitative assessment of the quality of each prediction in the form of Reliability Index value.		Aqueous solubility module provides the quantitative estimate of the compound’s solubility in water at 25°C (in terms of intrinsic solubility Log S<sub>0</sub>, mmol/ml) using a fragmental GALAS (<b>G</b>lobal, <b>A</b>djusted <b>L</b>ocally <b>A</b>ccording to <b>S</b>imilarity) model. The latter methodology allows the module to provide a quantitative assessment of the quality of each prediction in the form of Reliability Index value.

	'''Training set size:''' 4,764<br>		'''Training set size:''' 4,764<br>
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	<span style="font-size:8pt">		<span style="font-size:8pt">
	<nowiki>*</nowiki> - Articles reporting LogS<sub>w</sub> ~~models~~ by other authors were the predominant type among analyzed literature, meaning that each publication contained larger collections of experimental data (usually in the order of tens or hundreds compounds) compiled from corresponding original experimental articles.		<nowiki>*</nowiki> - Articles reporting the models of solubility in pure water (LogS<sub>w</sub>) by other authors were the predominant type among analyzed literature, meaning that each publication contained larger collections of experimental data (usually in the order of tens or hundreds compounds) compiled from corresponding original experimental articles. Original LogS<sub>w</sub> data had been converted to LogS<sub>0</sub> prior to modeling.
	</span>		</span>
	<br>		<br>
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	<br>		<br>
	{\| cellpadding="2" cellspacing="0" style="border-top:2px solid black; border-bottom:2px solid black"		{\| cellpadding="2" cellspacing="0" style="border-top:2px solid black; border-bottom:2px solid black"
	\|+ <b>Table 1.</b> ACD/LogS<sub>~~w</sub> (AB/LogS<sub>w~~</sub> ~~v2.0)~~ model performance statistics for ~~the~~ various fractions of the internal validation set.		\|+ <b>Table 1.</b> ACD/LogS<sub>0</sub> model performance statistics for various fractions of the internal validation set.
	\|-		\|-
	! style="border-bottom:1px solid black; background:#EAEAEA" width="150" \| Subset		! style="border-bottom:1px solid black; background:#EAEAEA" width="150" \| Subset
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	! style="border-bottom:1px solid black; background:#EAEAEA" width="100" \| <i>RMSE</i>		! style="border-bottom:1px solid black; background:#EAEAEA" width="100" \| <i>RMSE</i>
	\|-		\|-
	\| align="center" height="60" \| <i>RI</i> > 0.3 <br> N = 1,~~989~~		\| align="center" height="60" \| <i>RI</i> > 0.3 <br> N = 1,990

	\| align="center" \|		\| align="center" \|
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	\|}		\|}

	\| align="center" \| 0.85 \|\| align="center" \| 0.81		\| align="center" \| 0.83 \|\| align="center" \| 0.84
	\|-		\|-
	\| align="center" height="60" \| <i>RI</i> > 0.5 <br> N = 1,~~733~~		\| align="center" height="60" \| <i>RI</i> > 0.5 <br> N = 1,663

	\| align="center" \|		\| align="center" \|
	{\| cellpadding="0" cellspacing="0" style="width:80%; height:40px"		{\| cellpadding="0" cellspacing="0" style="width:80%; height:40px"
	\| style="color:white; background:#B9CDE5" align="right" width="84.8%" \| <b>84.8% </b> \|\| style="background:#EDF2F9" width="15.2%" \|		\| style="color:white; background:#B9CDE5" align="right" width="81.4%" \| <b>81.4% </b> \|\| style="background:#EDF2F9" width="18.6%" \|
	\|}		\|}

	\| align="center" \| 0.87 \|\| align="center" \| 0.75		\| align="center" \| 0.87 \|\| align="center" \| 0.77
	\|-		\|-
	\| align="center" height="60" \| <i>RI</i> > 0.75 <br> N = ~~593~~		\| align="center" height="60" \| <i>RI</i> > 0.75 <br> N = 567

	\| align="center" \|		\| align="center" \|
	{\| cellpadding="0" cellspacing="0" style="width:80%; height:40px"		{\| cellpadding="0" cellspacing="0" style="width:80%; height:40px"
	\| style="color:white; background:#B9CDE5" align="right" width="29.0%" \| <b>29.0% </b> \|\| style="background:#EDF2F9" width="71.0%" \|		\| style="color:white; background:#B9CDE5" align="right" width="27.7%" \| <b>27.7% </b> \|\| style="background:#EDF2F9" width="72.3%" \|
	\|}		\|}

	\| align="center" \| 0.94 \|\| align="center" \| 0.59		\| align="center" \| 0.93 \|\| align="center" \| 0.64
	\|}		\|}

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Kristina at 14:35, 21 January 2013

2013-01-21T14:35:01Z

← Older revision		Revision as of 14:35, 21 January 2013
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	# Indication of the prediction reliability along with the Reliability Index value		# Indication of the prediction reliability along with the Reliability Index value
	# "Configure" and "Train" buttons provide the means to select the training library for use in calculations and to add new data to that library. The name of the currently selected library is indicated with italic font.		# "Configure" and "Train" buttons provide the means to select the training library for use in calculations and to add new data to that library. The name of the currently selected library is indicated with italic font.
	~~# Estimated intrinsic solubility in water in S<sub>0</sub> (mg/ml) units~~
	# Up to 5 similar structures from the training set with experimental values		# Up to 5 similar structures from the training set with experimental values

Kristina: Created page with "==Overview==
This module predicts intrinsic solubility (LogS₀, mmol/ml) of a compound in water at 25°C using a set of >6,800 compounds. ===Features=== * C..."

2013-01-21T14:34:13Z

Created page with "==Overview== This module predicts intrinsic solubility (LogS0, mmol/ml) of a compound in water at 25°C using a set of >6,800 compounds. ===Features=== * C..."

New page

==Overview==
 

This module predicts intrinsic solubility (LogS0, mmol/ml) of a compound in water at 25°C using a set of >6,800 compounds.

===Features===
* Calculates a Reliability Index for every prediction
* Performs a similarity search and displays top 5 most similar structures from the training sets of the model
 

== Interface ==
 

[[Image:Logs0.png|center]]
 
# Quantitative estimate of the compound's intrinsic solubility in water
# Indication of the prediction reliability along with the Reliability Index value
# "Configure" and "Train" buttons provide the means to select the training library for use in calculations and to add new data to that library. The name of the currently selected library is indicated with italic font.
# Estimated intrinsic solubility in water in S0 (mg/ml) units
# Up to 5 similar structures from the training set with experimental values

'''Note''': Prediction reliability classification according to Reliability Index (RI) values:
* RI < 0.3 – Not Reliable,
* RI in range 0.3-0.5 – Borderline Reliability,
* RI in range 0.5-0.75 – Moderate Reliability,
* RI >= 0.75 – High Reliability
 

<div class="mw-collapsible mw-collapsed">

==Technical information==
 

<div class="mw-collapsible-content">
Aqueous solubility module provides the quantitative estimate of the compound’s solubility (Log Sw, mmol/ml and Sw mg/ml) in pure water at 25°C using a fragmental GALAS (Global, Adjusted Locally According to Similarity) model. The latter methodology allows the module to provide a quantitative assessment of the quality of each prediction in the form of Reliability Index value.

'''Training set size:''' 4,764 
'''Internal validation set size:''' 2,043 
'''Main sources of experimental data:'''
* Reference books:
** The Merck Index. An Encyclopedia of Chemicals, Drugs, and Biologicals, O'Neil, M.J., Smith, A., Heckelman, P.E., Budavari, S., Eds. 13th Edition, Merck & Co., Inc., Whitehouse Station, NJ, 2001
** Therapeutic Drugs, Dolery, C., Ed. 2nd Edition, Churchill Livingstone, New York, NY, 1999
** Clarke's Isolation and Identification of Drugs, Moffat, A.C., Jackson, J.V., Moss, M.S., Widdop, B., Eds. 2nd Edition, The Pharmaceutical Press, London, 1986
* Various articles from peer-reviewed scientific journals*


<nowiki>*</nowiki> - Articles reporting LogSw models by other authors were the predominant type among analyzed literature, meaning that each publication contained larger collections of experimental data (usually in the order of tens or hundreds compounds) compiled from corresponding original experimental articles.

 
====Internal Validation====
 
{| cellpadding="2" cellspacing="0" style="border-top:2px solid black; border-bottom:2px solid black"
|+ Table 1. ACD/LogSw (AB/LogSw v2.0) model performance statistics for the various fractions of the internal validation set.
|-
! style="border-bottom:1px solid black; background:#EAEAEA" width="150" | Subset
! style="border-bottom:1px solid black; background:#EAEAEA" width="210" | Coverage of the entire internal validation set (N=2,043)
! style="border-bottom:1px solid black; background:#EAEAEA" width="100" | R2
! style="border-bottom:1px solid black; background:#EAEAEA" width="100" | RMSE
|-
| align="center" height="60" | RI > 0.3 N = 1,989

| align="center" |
{| cellpadding="0" cellspacing="0" style="width:80%; height:40px"
| style="color:white; background:#B9CDE5" align="right" width="97.4%" | 97.4%  || style="background:#EDF2F9" width="2.6%" |  
|}

| align="center" | 0.85 || align="center" | 0.81
|-
| align="center" height="60" | RI > 0.5 N = 1,733

| align="center" |
{| cellpadding="0" cellspacing="0" style="width:80%; height:40px"
| style="color:white; background:#B9CDE5" align="right" width="84.8%" | 84.8%  || style="background:#EDF2F9" width="15.2%" |  
|}

| align="center" | 0.87 || align="center" | 0.75
|-
| align="center" height="60" | RI > 0.75 N = 593

| align="center" |
{| cellpadding="0" cellspacing="0" style="width:80%; height:40px"
| style="color:white; background:#B9CDE5" align="right" width="29.0%" | 29.0%  || style="background:#EDF2F9" width="71.0%" |  
|}

| align="center" | 0.94 || align="center" | 0.59
|}

</div>
</div>

ACD/LogS0 GALAS - Revision history

Kirilas at 10:11, 15 June 2017

Kirilas: /* Technical information */

Kirilas: /* Technical information */

Kristina at 14:35, 21 January 2013

Kristina: Created page with "==Overview== This module predicts intrinsic solubility (LogS0, mmol/ml) of a compound in water at 25°C using a set of >6,800 compounds. ===Features=== * C..."

Kristina: Created page with "==Overview==
This module predicts intrinsic solubility (LogS₀, mmol/ml) of a compound in water at 25°C using a set of >6,800 compounds. ===Features=== * C..."