Similarity search aims to search and scan a chemical database to identify those molecules that are most similar to a user-defined reference structure using some quantitative measures of intermolecular structural similarity [4 8].
As a starting point, his laboratory, which includes engineers, chemists, computer scientists, and physicists, developed DAEDALUS (DNA Origami Sequence Design Algorithm for User-defined Structures), an algorithm designed to automate the process of assembling DNA nanoparticles.
(DNA Origami Sequence Design Algorithm for User-defined Structures — not an exact match, but we'll forgive them).
A user-defined number of best-hit structural templates are used to model a 3D structure of the submitted sequence by MODELLER [ 89].
A time series algorithm is trained using "baseline" data to predict the vibration response, compare predictions to actual measurements collected on a potentially damaged structure, and calculate a user-defined damage indicator.
Our second formulation aims to reduce the running time and memory cost of the initial nucleotide-level alignment problem by sacrificing the sensitivity upon structures shorter than a user-defined threshold value.
*A TM value > 0.5 implies that the model has the correct topology [ 82]. **The STIV2 B204 structure in complex with AMPPCP PDBB: 4KFU) was used as a user-defined restraint.
If no such combination is found within a user-defined number of steps and attempts, the output will be the full atomic structure with least number of collisions observed over the course of this search.
Population structure was also assessed using the Bayesian clustering algorithm implemented in structure v. 2.2 [36], [36], which assigns individual multi-locus genotypes probabilistically to a user-defined number of clusters (K) [27].
A user-defined or a pre-defined design case can be selected interchangeably.
Then, a nonlinear viscoelastic constitutive model is implemented by means of a user-defined subroutine.
