Collura V, Higo J, Garnier J
Unité d'Ingénierie des Protéines, Biotechnologies, INRA, Jouy en Josas, France.
Protein Sci. 1993 Sep;2(9):1502-10. doi: 10.1002/pro.5560020915.
A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.
本文提出了一种用于蛋白质同源建模的蛋白质环建模方法。该方法采用了Higo等人的ESAP程序（Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33 - 43），基于快速蒙特卡罗模拟和模拟退火算法。该方法在免疫球蛋白、牛胰蛋白酶抑制剂和牛胰蛋白酶的不同环或肽段上进行了测试。预测结构是通过在300 K下蒙特卡罗模拟坐标的系综平均得到的，其具有最低的内能。建模前环的起始构象选择为完全伸展，并对末端残基的N、CA、C和O原子施加封闭的谐势。使用了具有联合原子表示的Robson和Platt（1986, J. Mol. Biol. 188, 259 - 281）的刚性几何势。我们证明这会产生在拉氏图允许区域内具有良好氢键和扭转角的环结构。对八个建模环评估的建模平均准确度为：主链原子的均方根偏差（rmsd）为1 Å，所有重原子的rmsd为2.3 Å。
