𝔖 Bobbio Scriptorium
✦   LIBER   ✦

A vectorized algorithm for calculating the accessible surface area of macromolecules

✍ Scribed by Huajun Wang; Cyrus Levinthal

Publisher
John Wiley and Sons
Year
1991
Tongue
English
Weight
378 KB
Volume
12
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

An algorithm is presented for calculating the solvent accessible surface area of proteins using a threedimensional grid. Since it requires only calculations based on single atomic positions, the algorithm is easy to be vectorized. It has been implemented on STlOO and may also be implemented on supercomputers like the CRAY or the CYBER. Results on several proteins indicate that its deviation from that of the Shake-Rupley algorithm is very small while the computation time is much reduced.

πŸ“œ SIMILAR VOLUMES

A new analytical method for computing so
A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients
✍ Shura Hayryan; Chin-Kun Hu; Jaroslav SkΕ™ivΓ‘nek; Edik Hayryane; Imrich PokornΓ½ πŸ“‚ Article πŸ“… 2005 πŸ› John Wiley and Sons 🌐 English βš– 191 KB

## Abstract In the calculation of thermodynamic properties and three‐dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent‐accessible surface area of macromolecules. Here, we propose a new analytical method for this purp

Calculating the electric potential of ma
Calculating the electric potential of macromolecules: A simple method for molecular surface triangulation
✍ Xiang Zhexin; Shi Yunyu; Xu Yingwu πŸ“‚ Article πŸ“… 1995 πŸ› John Wiley and Sons 🌐 English βš– 415 KB

An improved version of the "marching-cube" method' is proposed for molecular surface triangulation. This new algorithm involves fewer and simpler basic building blocks and avoids the artificial gaps of the original one. Moreover, to make it applicable to the boundary element method, the procedures f

Novel computer program for fast exact ca
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
✍ Oleg V. Tsodikov; M. Thomas Record Jr.; Yuri V. Sergeev πŸ“‚ Article πŸ“… 2002 πŸ› John Wiley and Sons 🌐 English βš– 115 KB

## Abstract New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of averag