Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
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DOI：
10.1002/(sici)1096-987x(19990130)20:2
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发表时间：
1999-01
影响因子：
3
通讯作者：
J. Weiser;P. Shenkin;W. Still
中科院分区：
文献类型：
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作者：
J. Weiser;P. Shenkin;W. Still
推导了一个快速分析公式，用于计算近似的原子和分子货车德瓦尔斯（vdWSA）和溶剂可及表面积（SASA），以及这些量相对于原子坐标的一阶和二阶导数。这种方法利用硬球的成对重叠项的线性组合，因此，我们称之为成对重叠项线性组合的LCPO方法。为了获得更高的性能，邻居列表缩减（NLR）被应用作为预处理步骤。18种不同大小（8-2366个原子）和类别（有机物，蛋白质，DNA和各种复合物）的化合物被选为代表性的测试案例。LCPO/NLR在SGI R10000/194 Mhz处理器上计算了SASA和青霉菌胃蛋白酶（一种具有2366个原子的蛋白质）的一阶导数，用时0.87 s（创建邻居列表用时0.22 s，NLR用时0.35 s，SASA和一阶导数用时0.30 s）。这似乎与以前报告的其他算法的时间相当或更好。vdWSAs与数值计算结果吻合良好：总分子表面积的相对误差范围为0.1至2.0%，平均绝对原子表面积偏差为0.3至0.7 μ m2。对于没有NLR的SASA，LCPO方法显示出总分子表面积的相对误差范围为0.4-9.2%，平均绝对原子表面积偏差为2.0-2.7 μ m2;使用NLR，相对分子误差范围为0.1 - 7.8%，平均绝对原子表面积偏差为1.6 - 3.0 μ m2。©1999 John Wiley & Sons，Inc. J Comput Chem 20：217-230，1999
A fast analytical formula was derived for the calculation of approximate atomic and molecular van der Waals (vdWSA), and solvent‐accessible surface areas (SASAs), as well as the first and second derivatives of these quantities with respect to atomic coordinates. This method makes use of linear combinations of terms composed from pairwise overlaps of hard spheres; therefore, we term this the LCPO method for linear combination of pairwise overlaps. For higher performance, neighbor‐list reduction (NLR) was applied as a preprocessing step. Eighteen compounds of different sizes (8–2366 atoms) and classes (organic, proteins, DNA, and various complexes) were chosen as representative test cases. LCPO/NLR computed the SASA and first derivatives of penicillopepsin, a protein with 2366 atoms, in 0.87 s (0.22 s for the creation of the neighbor list, 0.35 s for NLR, and 0.30 s for SASA and first derivatives) on an SGI R10000/194 Mhz processor. This appears comparable to or better than timings reported previously for other algorithms. The vdWSAs were in good agreement with the numerical results: relative errors for total molecular surface areas ranged from 0.1 to 2.0% and average absolute atomic surface area deviations from 0.3 to 0.7 Å2. For SASAs without NLR, the LCPO method exhibited relative errors in the range of 0.4–9.2% for total molecular surface areas and average absolute atomic surface area deviations of 2.0–2.7 Å2; with NLR the relative molecular errors ranged from 0.1 to 7.8% and the average absolute atomic surface area deviation from 1.6 to 3.0 Å2. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 217–230, 1999