Source 1primary paper2017Protein Science
Toolkit/elastic network model
elastic network model
Also known as: ENM
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The elastic network model (ENM) is a computational method for analyzing protein structural dynamics from an elastic network representation. In the cited PAS domain superfamily study, ENM was used to quantify residue fluctuations and vibrational patterns and to relate these dynamic features to sequence conservation, structural features, and biological function.
Usefulness & Problems
Why this is useful
ENM is useful for extracting protein dynamic information from structure-based models and for comparing fluctuation patterns across related protein groups. In the cited work, it enabled analysis of how PAS domain dynamics align with conserved residues and functional classification.
Source:
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
Source:
The result showed that the proteins with same function could be grouped by sequence similarity
Problem solved
This method helps address the problem of linking protein sequence and structure to functional evolution through dynamics. In the PAS domain study, it was applied to identify whether conserved residues and distinct functional groups exhibit characteristic fluctuation and vibrational signatures.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
normal-mode-based analysis of protein vibrational dynamicsnormal-mode-based analysis of protein vibrational dynamicsresidue fluctuation analysis from an elastic network representationresidue fluctuation analysis from an elastic network representationTarget processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: builder
The available evidence states that protein dynamics were analyzed using an elastic network model, implying a structure-based computational workflow rather than an experimental reagent. The provided material does not specify software implementation, parameterization, input structure requirements, or integration with other modeling steps.
The supplied evidence supports ENM use in a PAS domain superfamily analysis but does not provide broader benchmarking, predictive accuracy metrics, or comparisons to alternative dynamics methods. Practical performance characteristics, parameter sensitivity, and generalizability beyond this study are not described in the provided evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
Approval Evidence
1 source1 linked approval claimfirst-pass slug elastic-network-model
The protein dynamics were analyzed using elastic network model (ENM)
Source:
sequence structure dynamics function connectionsupports
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
Source:
Comparisons
Source-backed strengths
The cited study reports that residues conserved by sequence and structure analyses generally had lower fluctuation than other residues across three PAS functional groups. It also found statistically significant differences in vibrational patterns among PAS functional groups and a strong correlation between conserved-residue fluctuation and biological function within each group.
Compared with free-energy calculations
elastic network model and free-energy calculations address a similar problem space.
Shared frame: same top-level item type
Compared with mathematical model
elastic network model 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 SwiftLib
elastic network model and SwiftLib address a similar problem space.
Shared frame: same top-level item type
Ranked Citations
- 1.