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regsys [2013/02/27 09:04]
rkiss
regsys [2013/10/19 13:36] (current)
rkiss [Process outline]
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 ====== Mcule Advanced Curation (MAC) ====== ====== Mcule Advanced Curation (MAC) ======
  
-The mcule database is curated by MAC (Mcule Advanced Curation) that involves a rigorous molecule registration system based on more than 80 structural checks, standardization, preparation and correction steps. MAC guarantees high quality search results and avoids common errors arising from mis-drawn and incorrect structures that can critically affect the quality of computational calculations and the efficiency of experimental results.+The mcule database is curated by **MAC (Mcule Advanced Curation)** that involves a rigorous molecule registration system based on more than 80 structural checks, standardization, preparation and correction steps. MAC guarantees high quality search results and avoids common errors arising from mis-drawn and incorrect structures that can critically affect the quality of computational calculations and the efficiency of experimental results.
  
-==== Quality is important ====+**Key features of MAC:** high level data curation, stereochemical standardization, robust novelty check and isomer detection, correct handling of salts & organometallics
  
-The design of screening libraries and the development of predictive drug discovery models all start with a high quality database. Chemical correctness is crucial because mis-drawn and imperfectly defined structures result in incorrect models, misleading predictions and inconsistent hits. Problematic structures should therefore be eliminated at the earliest possible stage from a drug discovery pipeline.+Continue reading for more information about MAC, or check our presentations from the 244th National Meeting of American Chemical Society:
  
 +[[http://mcule-blog.s3.amazonaws.com/acs12/mcule_ACS12_Phi_libraries.pdf|Evaluation of data quality in currently available compound libraries (slides)]]
  
-The mcule structure registration system is primarily designed to handle chemical structures coming from different data sources, mainly from chemical suppliers, and load the structures into the mcule database. This is a non-trivial task which requires a careful structure check and preparation procedureTo reach a high curation level, the registration system should ensure database quality in terms of structure correctness, uniqueness and reliability as well as maintain a high level of data standardization.+[[http://mcule-blog.s3.amazonaws.com/acs12/mcule_ACS12_libraries.jpg|Evaluation of data quality in currently available compound libraries (poster)]]
  
-All molecules with an MCULE ID have been processed by the mcule structure registration system. User uploaded molecules are not processed by the mcule structure registration system by default. We will enable this option in future. 
  
-**Key features:** high level data curation, stereochemical standardization, robust novelty check and isomer detection, handling salts & organometallics+==== Quality is important ====
  
-===Registration challenges===+The design of screening libraries and the development of predictive drug discovery models **all start with a high quality database**. Chemical correctness is crucial because mis-drawn and imperfectly defined structures result in incorrect models, misleading predictions and inconsistent hits. Problematic structures should therefore be eliminated at the earliest possible stage from a drug discovery pipeline. 
 + 
 +The mcule structure registration system is primarily designed to correctly handle chemical structures coming from different data sources, mainly from chemical suppliers, and load the structures into the mcule database. This is a non-trivial task which requires a careful structure check and preparation procedure. To reach a high curation level, the registration system should ensure database quality in terms of structure correctness, uniqueness and reliability as well as maintain a high level of data standardization. 
 + 
 +**All molecules with an MCULE ID have been processed by MAC**. User uploaded molecules are not processed by MAC by default. We plan to enable this option in future. 
 + 
 +==== Registration challenges ====
  
  
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 ===== Process outline ===== ===== Process outline =====
  
-The whole registration process can be divided into seven different stages. It begins with the revision of stereo configurations, structure check/preparation steps (stage A, B) followed by component separation (stage C). Thereafter component uniqueness is checked and mcule IDs are assigned (stage D, E). This is performed with or without considering tautomerism and protonation, resulting the assignment of tautomer and protonation state independent [[mculeid|compound identifiers]] (stage D) as well as tautomer and protonation state dependent [[mculeid|structure identifiers]] (stage E). Finally, based on component identity, multicomponent entries are also registered at both the tautomer and protonation state independent (stage F) and dependent levels (stage G).+The whole registration process can be divided into seven different stages. It begins with the revision of stereo configurations, structure check/preparation steps (stage A, B) followed by component separation (stage C). Thereafter component uniqueness is checked and mcule IDs are assigned (stage D, E). This is performed with or without considering tautomerism and protonation, resulting the assignment of tautomer and protonation state independent [[structurelevels|compound identifiers]] (stage D) as well as tautomer and protonation state dependent [[structurelevels|structure identifiers]] (stage E). Finally, based on component identity, multicomponent entries are also registered at both the tautomer and protonation state independent (stage F) and dependent levels (stage G).
  
 |Stage A |Enforcing [[stereonotations|standard stereo representation]]; non-standard stereo notations are changed, unreliable part of stereo configurations is removed (after consulting with chemical supplier) | |Stage A |Enforcing [[stereonotations|standard stereo representation]]; non-standard stereo notations are changed, unreliable part of stereo configurations is removed (after consulting with chemical supplier) |
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 As a result, input entries as well as their components are registered at two levels: tautomer and protonation state independent [[structurelevels|compound level]] with tautomer detection and tautomer and protonation state dependent [[structurelevels|structure level]] without tautomer detection. As a result, input entries as well as their components are registered at two levels: tautomer and protonation state independent [[structurelevels|compound level]] with tautomer detection and tautomer and protonation state dependent [[structurelevels|structure level]] without tautomer detection.
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 ===== Registration process ===== ===== Registration process =====
  
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 In most cases the system is also capable of identifying the main components, which can serve as the input set for virtual screens. In most cases the system is also capable of identifying the main components, which can serve as the input set for virtual screens.
  
-You can see below the index page of compound [[https://mcule.com/MCULE-3198812899|MCULE-3198812899]]. This is a maleic and/or fumaric acid salt+You can see below the index page of compound [[https://mcule.com/MCULE-3198812899/|MCULE-3198812899]]. This is a maleic and/or fumaric acid salt
 (uncertainty is marked by crossed double bond). Counter ions are marked, and component multiplicities are assigned correctly by the system. (uncertainty is marked by crossed double bond). Counter ions are marked, and component multiplicities are assigned correctly by the system.
  
 {{:regsys:reg_sys_12.png|}} {{:regsys:reg_sys_12.png|}}
regsys.1361952297.txt.gz · Last modified: 2013/02/27 09:04 by rkiss