This textbook is designed for an undergraduate course in structural analysis and design as well as a follow up course on numerical (matrix-based) methods for structural analysis, i.e. introduction to finite element analysis. The book has ten chapters.
We generated synthetic images that are slight translations of each other and added Gaussian noise to the frames (Fig. S8A). For each translation amount, we compute the motion between the two frames over 4,000 runs. We compute the sample covariance matrix over the runs as a measure of the ground-truth noise level. We also used our noise analysis to estimate the covariance matrix at the points denoted in red.
Evolutionary conservation: Generally speaking, functional regions on protein surfaces are usually more evolutionarily conserved than other regions, but the study on antigen crystal structures draws opposite conclusion. Statistical test reveals that evolutionary conservation can significantly distinguish epitopes from non-epitope region . In order to calculate conservation scores, the primary sequence of the antigen chain we want to predict is aligned to the non-redundant protein database by using BLAST program (round of iteration is set to 3), and a position specific scoring matrix (PSSM) is returned. Then, the conservation score of the residue at the sequence position i is calculated by following function:
We further use the paired t-test to test differences between different methods, in which the predicted AUC scores of the test structures are used. Since the statistical analysis usually requires a great number of samples, the limited number of structures in the study leads to no statistical significance (p-value > 0.05). 1e1e36bf2d