Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets

• Published in: Journal of chemical information and modeling Vol. 50; no. 3; pp. 339 - 348
• Main Authors: Hussain, Jameed, Rea, Ceara
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 22.03.2010
• Subjects: Algorithms; Analytical chemistry; Biological and medical sciences; Chemical compounds; Chemical Information; Databases, Factual; Drug Discovery - methods; General pharmacology; Medical sciences; Molecular structure; Pharmaceutical technology. Pharmaceutical industry; Pharmacology. Drug treatments; Structure-Activity Relationship; Very large databases; Screening; Structure activity relation; Pharmaceutical industry; Data structure; Chemical structure
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/ci900450m

Modern drug discovery organizations generate large volumes of SAR data. A promising methodology that can be used to mine this chemical data to identify novel structure−activity relationships is the matched molecular pair (MMP) methodology. However, before the full potential of the MMP methodology can be utilized, a MMP identification method that is capable of identifying all MMPs in large chemical data sets on modest computational hardware is required. In this paper we report an algorithm that is capable of systematically generating all MMPs in chemical data sets. Additionally, the algorithm is computationally efficient enough to be applied on large data sets. As an example the algorithm was used to identify the MMPs in the ∼300k NIH MLSMR set. The algorithm identified ∼5.3 million matched molecular pairs in the set. These pairs cover ∼2.6 million unique molecular transformations.