Related Experiment Video
Updated: Feb 7, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
TopoFF: MOF structure prediction using specifically optimized blueprints
1Computational Materials Chemistry Group, Lehrstuhl für Anorganische Chemie 2, Ruhr-Universität Bochum, Bochum, Germany. rochus.schmid@rub.de.
Abstract:
For the structure prediction of MOFs and related crystalline framework materials we have proposed the Reversed Topological Approach (RTA), where the default embedding of a topology is used as a blueprint. The optimal rotational insertion of the building blocks (BBs) at the fixed vertex positions of the blueprint is performed by minimizing the target function of the average angle deviation (AAD). Here we extend this idea by pre-optimizing the maximum symmetry embedding of a topology in order to minimize the overall mean AAD for the given set of BBs. By this fast and essentially parameter-free topoFF method, the vertex positions and cell parameters of the blueprint are further optimized in order to fit the structural needs of the BBs, which speeds up the overall search for the most energetically favorable structure. In addition, different topologies can be ranked in a quantitative and intuitive way. The definition and implementation of topoFF is explained and its application for the RTA-based structure prediction of MOFs is demonstrated with a number of instructive examples.
Related Concept Videos
Predicting Molecular Geometry
Prediction Intervals
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.
Optimal Foraging
Protein and Protein Structure
A protein's shape is critical to its function. For example, an enzyme...
Optimization Problems
End Point Prediction: Gran Plot
For potentiometric titration, the Gran plot is created by plotting...

