Related Experiment Video
Updated: Aug 15, 2026

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
Published on: March 1, 2022
Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root
Federico Fogolari1, Silvio C E Tosatto
1Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4, 33100 Udine, Italy. ffogolari@mail.dstb.uniud.it
Abstract:
Accurate free energy estimation is needed in many predictive tasks. The molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be accurate. However, the correlation between the estimated free energy and the distance (e.g., root mean square deviation [RMSD]) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In this paper, a protocol for MM/PBSA free energy estimation is designed and tested on several loop decoy sets. We show that further integration of MM/PBSA free energy estimator with the colony energy approach makes the correlation between the free energy and RMSD from the native structure apparent, for the test sets on which it could be applied. Our results suggest that (1) the MM/PBSA free energy estimator is able to detect native-like structures for most decoy sets, and (2) application of the colony energy approach greatly hampers the MM/energy strong dependence on minor conformational changes.
Related Concept Videos
Root Mean Square
For example, consider the velocity of gas molecules in a container. The gas molecules are moving in different directions, which might impart positive and negative...
Empirical Method to Interpret Standard Deviation
This rule is used widely in statistics to calculate the proportion of data values...
Mean Absolute Deviation
Let us consider a dataset containing the number of unsold cupcakes in five shops: 10, 15, 8, 7, and 10. Initially, calculate the sample mean. Then calculate the deviation, or the difference, between each data value and the mean. Next, the absolute values of these deviations are added and divided by the sample size to...
Decision Making: P-value Method
First, a specific claim about the population parameter is proposed. The claim is based on the research question and is stated in a simple form. Further, an opposing statement to the claim is also stated. These statements can act as null and alternative hypotheses: a null hypothesis would be a neutral statement while the alternative hypothesis can have a...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Correlation of Experimental Data
For example, a spherical particle moving through a viscous fluid experiences drag. Dimensional analysis shows that the drag force depends on the particle's diameter, velocity, and...

