RMSD of the C-alpha carbon atoms of MMP-2 (PDB code: 1HOV) for the equilibration trajectories.Ilenia GiangrecoGianluca LattanziOrazio NicolottiMarco CattoAntonio LaghezzaFrancesco LeonettiAngela StefanachiAngelo Carotti
从同源性最强的序列开始,对于包含特定配体的蛋白质结构,经过与AlphaFold2模型的全局和局部两次结构比对(局部结构比对给出local RMSD值),将配体分子“移植”至AlphaFold2模型中。如果配体含有不同的构象,则分别地被记录于AlphaFill模型中。 随后,作者...
•RMSD(Root-Mean-Square Deviation):用于衡量预测结构与实验结构之间的差异程度。 •GDT(Global Distance Test):通过计算预测结构与实验结构之间的最优配对原子之间的距离,评估两者的相似性。 •MolProbity评分:综合考虑了蛋白质结构的几何、电荷和非法构象等因素,用于评估结构的合理性。 使用方法 模型CIF模块可以通...
and (ii) all the additional conformations exhibit a lower root-mean-square-deviation (1.97 ppm < or = rmsd < or = 2.13 ppm), between computed and observed 13C(alpha) chemical shifts, than the rmsd (2.32 ppm) computed for the starting conformation from which this additional set was derived...
rmsd root-mean-square deviation(sroot-mean-square deviation(sThe distribution of the C 伪-C 伪 distances between residues separated by three to 30 amino acid residues is highly characteristic of protein folds and makes it possible to identify them from a straightforward comparison of the distance...
2.1 and 1.8 angstrom Average C[sub alpha] RMSD Structure Predictions on Two Small Proteins...Presents several model predictions on the 36-mer villin headpiece domain (HP-36) and the 65-mer structured region of ribosomal protein (S15). Approach of the Rosetta protein folding algorithm; Simulation...
(ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed $$ {}^{13}{\\text{C}}^{{{\\up...
The RMSD, radius of gyration, and RMSF values were higher for the G555F mutant than the FGA wild type protein. Overall, the results support these vitamins' potential as a therapeutic and anti-amyloidogenic agent for FGA renal amyloidosis.Pande, Monu...