Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels

doi:10.3390/a1020183

This article is

freely available
re-usable

Algorithms 2008, 1(2), 183-200; doi:10.3390/a1020183

Article

Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels

Sergei V. Trepalin* and Alexander V. Yarkov

Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432, Chernogolovka, Moscow Region, Russia

* Author to whom correspondence should be addressed.

Received: 23 October 2008; in revised form: 23 November 2008 / Accepted: 5 December 2008 / Published: 18 December 2008

(This article belongs to the Special Issue Algorithms and Molecular Sciences)

Download PDF Full-Text [312 KB, uploaded 18 December 2008 14:12 CET]

Abstract: A new algorithm for divisive hierarchical clustering of chemical compounds based on 2D structural fragments is suggested. The algorithm is deterministic, and given a random ordering of the input, will always give the same clustering and can process a database up to 2 million records on a standard PC. The algorithm was used for classification of 1,183 antibiotics mixed with 999,994 random chemical structures. Similarity threshold, at which best separation of active and non active compounds took place, was estimated as 0.6. 85.7% of the antibiotics were successfully classified at this threshold with 0.4% of inaccurate compounds. A .sdf file was created with the probe molecules for clustering of external databases.

Keywords: Molecular structure; hierarchical clustering; algorithm; classification of antibiotics

Supplementary Files

Supplementary File 1:
TXT-Document (TXT, 1 KB)
Supplementary File 2:
ZIP-Document (ZIP, 2 KB)
Supplementary File 3:
ZIP-Document (ZIP, 49179 KB)
Supplementary File 4:
ZIP-Document (ZIP, 45978 KB)
Supplementary File 5:
ZIP-Document (ZIP, 38871 KB)
Supplementary File 6:
ZIP-Document (ZIP, 278089 KB)

Article Statistics

Click here to load and display the download statistics.

Cite This Article

MDPI and ACS Style

Trepalin, S.V.; Yarkov, A.V. Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels. Algorithms 2008, 1, 183-200.

AMA Style

Trepalin SV, Yarkov AV. Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels. Algorithms. 2008; 1(2):183-200.

Chicago/Turabian Style

Trepalin, Sergei V.; Yarkov, Alexander V. 2008. "Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels." Algorithms 1, no. 2: 183-200.

Algorithms EISSN 1999-4893 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert