FEP+ Panel — Analysis Tab

Analysis Tab Features

• Results table

Results table

Chain	Chain name
Mutation	Mutation, given in terms of the original residue and the mutant residue for each residue that is mutated.
FEP	Free energy difference (ΔΔG) in kcal mol−1 between two mutants directly connected in the map, including error estimate. ΔΔG is estimated with the Bennett Acceptance Ratio method. The error is the analytical statistical uncertainty estimate for the calculated Bennett ΔΔG. The error estimate is calculated based on the assumption that all the important regions of the phase space have been sampled, and usually it estimates the real error in the predicted free energy. If the error is higher than is considered reasonable, a warning symbol is displayed next to the error. These estimates rely only on data for the perturbation of the two mutants, and not on any other perturbation in the graph.
Cycle Closure	Cycle closure prediction of the free energy difference between two mutants and error estimate. The cycle closure algorithm takes the Bennett ΔΔG of all the pairs of mutants connected in the graph as input, and calculates the statistically most proper values of ΔΔG using the maximal likelihood method. The Bennett ΔΔG results may have hysteresis, while the Cycle Closure Corrected ΔΔG results do not have hysteresis, i.e. the free energy difference between any pair of mutants is independent of the path. The error estimate is calculated from the Bennett ΔΔG for all the pairs of mutants connected in the graph, and it is related to the hysteresis of the Bennett ΔΔG of the closed thermodynamic cycle.
Energy Conv.	Classification of energy convergence for the edge as GOOD or BAD. This classifier tracks the rate at which both FEP legs (solvent and complex) converge, measured in the last nanosecond (ns) of the simulation. GOOD—convergence rate is less than 0.3 kcal mol−1 ns−1. BAD—convergence rate exceeds 0.3 kcal mol−1 ns−1. Note: this is a beta feature, and the classifications may change in future.
REST Exch.	Classification of replica exchange density profiles as GOOD or BAD. A good profile is one in which all replicas are sampled adequately in all lambda windows.This classifier monitors the mixing of replicas throughout the FEP simulation and can be visualized through a PDF report of each edge. Replica mixing is assigned a score from 0 to 1, where one is perfect mixing while zero is no mixing. GOOD—mixing score of both legs, solvent and complex, is greater than 0.15 FAIR—mixing score of one of the legs is greater than 0.15, the other is less than 0.15 BAD—mixing score of both legs, solvent and complex, is less than 0.15 Note: this is a beta feature, and the classifications may change in future.
CCC Conv.	Classification of cycle closure hysteresis, based on the effect of random omission of edges on the hysteresis. This is the same classification as in the Map tab, when a perturbation is marked as bad. Note: this is a beta feature, and the classifications may change in future.
Similarity	This column displays the similarity score. It is not displayed by default.
Edge Analysis	Click the View button to display an analysis for the edge defined in this row, in the FEP+ — Analysis Panel.
Complex Trajectory	This column displays the total simulation time for the complex leg. The time is a link (in blue) which you can click to view the trajectory for the complex leg in the Trajectory Player
Solvent Trajectory	This column displays the total simulation time for the solvent leg. The time is a link (in blue) which you can click to view the trajectory for the solvent leg in the Trajectory Player
Fragment Trajectory	This column displays the total simulation time for the fragment leg. The time is a link (in blue) which you can click to view the trajectory for the fragment leg in the Trajectory Player

Related Topics

• FEP+ Panel
• Protein FEP+ Best Practices
• FEP Protein Mutation Panel
• FEP+ Panel — Analysis Tab
• Trajectory Player