The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
✍ Scribed by Frank Eisenhaber; Philip Lijnzaad; Patrick Argos; Chris Sander; Michael Scharf
- Publisher
- John Wiley and Sons
- Year
- 1995
- Tongue
- English
- Weight
- 986 KB
- Volume
- 16
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
The double cubic lattice method (DCLM) is an accurate and rapid approach for computing numerically molecular surface areas (such as the solvent accessible or van der Waals surface) and the volume and compactness of molecular assemblies and for generating dot surfaces. The algorithm has no special memory requirements and can be easily implemented. The computation speed is extremely high, making interactive calculation of surfaces, volumes, and dot surfaces for systems of 1000 and more atoms possible on single-processor workstations. The algorithm can be easily parallelized. The DCLM is an algorithmic variant of the approach proposed by Shrake and Rupley (J. Mol. Biol., 79,351-371,1973). However, the application of two cubic lattices-one for grouping neighboring atomic centers and the other for grouping neighboring surface dots of an atom-results in a drastic reduction of central processing unit (CPU) time consumption by avoiding redundant distance checks.