Department of Mathematics, Iowa State University, Ames, IA 50011, USA.
Bull Math Biol. 2011 Dec;73(12):2809-36. doi: 10.1007/s11538-011-9644-6. Epub 2011 Mar 18.
We propose a new approach to the problem of determining an ensemble of protein structures with a set of interatomic distance bounds in NMR protein modeling. Similarly to X-ray crystallography, we assume that the protein has an equilibrium structure and the atoms fluctuate around their equilibrium positions. Then, the problem can be formulated as a generalized distance geometry problem, to find the equilibrium positions and maximal possible fluctuation radii for the atoms in the protein, subject to the condition that the fluctuations should be within the given distance bounds. We describe the scientific background of the work, the motivation of the new approach and the formulation of the problem. We develop a geometric buildup algorithm for an approximate solution to the problem and present some preliminary test results as a first step concept proofing. We also discuss related theoretical and computational issues and potential impacts of this work in NMR protein modeling.
我们提出了一种新的方法来解决在 NMR 蛋白质建模中确定具有一组原子间距离约束的蛋白质结构集合的问题。与 X 射线晶体学类似，我们假设蛋白质具有平衡结构，原子在其平衡位置周围波动。然后，该问题可以被表述为一个广义距离几何问题，以找到蛋白质中原子的平衡位置和最大可能的波动半径，同时满足波动应在给定的距离约束内的条件。我们描述了这项工作的科学背景、新方法的动机以及问题的表述。我们开发了一种几何构建算法来求解该问题的近似解，并给出了一些初步的测试结果作为概念验证的第一步。我们还讨论了相关的理论和计算问题以及这项工作在 NMR 蛋白质建模中的潜在影响。
