A dynamic data structure for flexible molecular maintenance and informatics.
BACKGROUND
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.


BACKGROUND
http://www.cs.utexas.edu/~bajaj/cvc/software/DPG.shtml.
Department of Computer Science, University of Texas at Austin, Austin, TX, USA. bajaj@cs.utexas.edu
Chandrajit
C
Bajaj
Rezaul Alam
RA
Chowdhury
Muhibur
M
Rasheed
D019295:Computational Biology; D015195:Drug Design; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
D011506:Proteins