A dynamic data structure for flexible molecular maintenance and informatics

• Published in: Bioinformatics Vol. 27; no. 1; pp. 55 - 62
• Main Authors: Bajaj, Chandrajit, Chowdhury, Rezaul Alam, Rasheed, Muhibur
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.01.2011
• Subjects: Biological and medical sciences; Computational Biology; Drug Design; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Molecular; Molecular Conformation; Molecular Dynamics Simulation; Original Papers; Protein Conformation; Proteins - chemistry; Data; Maintenance; Molecular structure; Data structure; Dynamics
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btq627

Motivation: We present the 'Dynamic Packing Grid' (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations. Results: DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements. Availability: http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml Contact: bajaj@cs.utexas.edu Supplementary information: Supplementary data are available at Bioinformatics online.