Ul Islam Rifat Nawaz, Mitra Debanjan, Sen Gupta Parth Sarthi, Banerjee Sahini, Mondal Buddhadev, Bandyopadhyay Amal Kumar
Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India.
Department of Biotechnology, TheUniversity of Burdwan, East Burdwan, West Bengal, India.
Bioinformation. 2018 Dec 22;14(9):525-529. doi: 10.6026/97320630014525. eCollection 2018.
Global minimal structure of protein/enzyme is energetically compromised that maintains an intricate balance between the rigidity and the flexibility. Such a state makes it interactive to its ligand molecules. Although protein data bank files (PDB) may have achieved the state, in many situations minimization has been crucial to overcome unwanted steric clashes, and other conformational strains. It is more so, when orthologous PDB structures that are intended in a given study, show variations in resolution, R-factor, shell-water contents, loop characteristics etc. Here, a fully automated procedure of minimization would be highly useful. AUTOMINv1.0 is such an automation of minimization that runs on any number of structure files with any number of chains in them along with the inclusion of selective/non-selective shell-waters interacting with polar and or non-polar atom-types of protein. Comparison of the mean binaryitems of salt-bridges of minimized and un-minimized structures (chains > 100) of nucleoside diphosphate kinase from mimi virus shows dramatic improvements in the earlier. Again, the mean steric clashes of 2AZ3.pdb are reduced upon minimization. Remarkably, the observed steric clashes between shell-waters and atom-types of protein are seen to be removed upon minimization. Taken together, AUTOMINv1.0 is an automation of minimization that finds applications in structural bioinformatics.
蛋白质/酶的全局最小结构在能量上是不稳定的，它在刚性和柔韧性之间保持着复杂的平衡。这种状态使其与配体分子具有相互作用。尽管蛋白质数据库文件（PDB）可能已达到这种状态，但在许多情况下，最小化对于克服不必要的空间冲突和其他构象应变至关重要。当给定研究中预期的直系同源PDB结构在分辨率、R因子、壳层水含量、环特征等方面表现出差异时，情况更是如此。在这里，一个完全自动化的最小化程序将非常有用。AUTOMINv1.0就是这样一种最小化自动化程序，它可以在任意数量的结构文件上运行，这些文件包含任意数量的链，同时还包括与蛋白质的极性和/或非极性原子类型相互作用的选择性/非选择性壳层水。对米米病毒核苷二磷酸激酶最小化和未最小化结构（链数>100）的盐桥平均二元项进行比较，结果显示前者有显著改善。同样，2AZ3.pdb的平均空间冲突在最小化后减少。值得注意的是，最小化后，观察到的壳层水与蛋白质原子类型之间的空间冲突消失了。综上所述，AUTOMINv1.0是一种最小化自动化程序，在结构生物信息学中有应用价值。
