Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets

Journal of Chemical Information and Modeling

Volumn 50, Issue 3, 2010, Pages 339-348

  Hussain, Jameed ^a   Rea, Ceara ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

CHEMICAL DATA SET; COMPUTATIONALLY EFFICIENT; DRUG DISCOVERY; IDENTIFICATION METHOD; LARGE DATASETS; MOLECULAR PAIRS; MOLECULAR TRANSFORMATION; NOVEL STRUCTURES;

COMPUTATIONAL EFFICIENCY;

ALGORITHM; ARTICLE; DRUG DEVELOPMENT; FACTUAL DATABASE; METHODOLOGY; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; DATABASES, FACTUAL; DRUG DISCOVERY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77949848865     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900450m     Document Type: Article

References (27)

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17. SMARTS used: "[*]!!=[*]".
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20. Compounds were removed if they were found to be mixtures after an in-house desalting procedure was applied (56 compounds) or if they contain more than 100 non-hydrogen atoms such as peptides (7 compounds).
21. Compounds were removed if they contained nonstandard isotopes (8 compounds) or if they did not have a chemically tractable bond [C-(N, O, S)] (42 compounds) or contained nonorganic elements (that is, not in the set (C, N, O, P, S, halogen, B, or Si) (46 compounds).
22. The calculation was performed on a single core of a dual core Intel (R) Xeon(TM) 3.00 GHz cpu (2048 Kb cache size).
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24. SMARTS changed from "[*]!!=[*] "to"[#6+0;!$(*=,#[!#6])]!!=!#[*]".
25. It was noted by one of the reviewers that a maximum size parameter of 10 non-hydrogen atoms will miss some (perhaps key) transforma-tions (e.g., C1(C2=CC=CC=C2)=CC=CC=C1 (biphenyl) to C1(C2= CC=CC=C2C3)=C3C=CC=C1 (fluorene)). Therefore, an appropri-ate value for the maximum size parameter needs to be chosen. This depends on the size of the dataset and the size of the molecular transformations one would like to find.
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27. Determined by calculating the average time to retrieve the MMPs for 20 randomly selected compounds from the database. The BENCHMARK function available within MySQL was used to determine the time it took to perform the SQL query (a thousand times) to find the MMPs (for each of the 20 twenty compounds). The average time to run a thousand SQL queries was 0.88 seconds which equates to an average time of 0.00088 seconds for a single SQL query to retrieve the MMPs for a database compound.