Source 1primary paper2020Proteins Structure Function and Bioinformatics
Toolkit/free-energy calculations
free-energy calculations
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Free-energy calculations are an in silico prediction method used in the rational design of human Caspase-2 mutants. In the cited study, they were applied alongside sequence and structural comparisons of Caspase-2 and Caspase-3 to predict effects of active-site mutations on substrate recognition and to support engineering of broader amino-acid acceptance.
Usefulness & Problems
Why this is useful
This computational method is useful for prioritizing protease active-site mutations before experimental testing. In the cited Caspase-2 study, it supported prediction of how mutations would alter recognition of branched amino acids and guided mutant selection for in vitro validation.
Problem solved
It addresses the problem of predicting how specific active-site mutations will affect substrate recognition in a protease. In the reported application, it helped rationally design human Caspase-2 variants with increased acceptance of branched amino acids relative to the unmutated enzyme.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Target processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: builder
In the cited work, free-energy calculations were used together with sequence and structural comparisons of Caspase-2 and Caspase-3 during in silico mutant design. The available evidence indicates subsequent in vitro confirmation of two proposed human Caspase-2 active-site mutants, but it does not specify the exact free-energy protocol, force field, or software implementation.
The evidence is limited to a single reported application in human Caspase-2 from one study. The supplied evidence does not report quantitative accuracy, computational cost, software details, or validation across multiple proteins or mutation classes.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
Two active-site mutations in human Caspase-2 increased recognition of branched amino acids relative to the unmutated protease.
Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants.
The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Both engineered Caspase-2 mutants showed enhanced activity toward branched amino acids and also toward smaller unbranched amino acids.
Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids.
Approval Evidence
1 source1 linked approval claimfirst-pass slug free-energy-calculations
their effect was additionally predicted using free-energy calculations
Source:
computational designsupports
The engineered protease mutants were designed in silico using sequence and structural comparisons of Caspase-2 and Caspase-3 together with free-energy calculations.
These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations.
Source:
Comparisons
Source-backed strengths
The method contributed to a rational design workflow that combined sequence comparison, structural comparison, and energetic prediction. In vitro experiments confirmed the simulation results for the two proposed Caspase-2 mutants, and two active-site mutations increased recognition of branched amino acids relative to wild-type Caspase-2.
Compared with mathematical model
free-energy calculations and mathematical model address a similar problem space.
Shared frame: same top-level item type
Strengths here: looks easier to implement in practice.
Compared with QM calculations
free-energy calculations and QM calculations address a similar problem space.
Shared frame: same top-level item type
Strengths here: looks easier to implement in practice.
Compared with SwiftLib
free-energy calculations and SwiftLib address a similar problem space.
Shared frame: same top-level item type
Ranked Citations
- 1.