A general, fast, and exact optimization, called neighbor-list ## Ž . reduction NLR , is presented, which can be used to accelerate the computation of hard-sphere molecular surface areas. NLR allows selected neighbors of a central atom to be removed from the computation in a preprocessing step, thu
✦ LIBER ✦
Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas
✍ Scribed by Weiser, J�rg; Weiser, Armin A.; Shenkin, Peter S.; Still, W. Clark
- Publisher
- John Wiley and Sons
- Year
- 1998
- Tongue
- English
- Weight
- 78 KB
- Volume
- 19
- Category
- Article
- ISSN
- 0192-8651
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We analyze the contact distance distributions between nonbonded atoms in known protein structures. A complete set of van der Waals (VDW) radii for 24 protein atom types and for crystal-bound water is derived from the contact distance distributions of these atoms with a selected group of apolar atoms