Source 1primary paper2022Research Square (Research Square)
Toolkit/designed decoy peptides targeting CIB1
designed decoy peptides targeting CIB1
Also known as: novel peptides, top five designed peptides
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Designed decoy peptides targeting CIB1 are in silico engineered variants of the reference peptide UNC10245092 generated by residue scan methodology to bind CIB1. In the reported computational study, top candidates were prioritized by predicted binding free energy, evaluated by AMBER molecular dynamics simulations, and were predicted to interfere with RAF–CIB1 binding; mutant 2 showed stronger predicted interactions with CIB1 than the reference peptide.
Usefulness & Problems
Why this is useful
These peptides are useful as computationally prioritized decoy binders for probing or potentially obscuring CIB1-mediated protein interactions. The study specifically positions them as candidates to prevent RAF binding to CIB1, which is relevant to investigating CIB1 function in triple-negative breast cancer progression.
Problem solved
The tool addresses the problem of designing peptide-based competitors against CIB1 starting from an existing reference peptide, UNC10245092. It also addresses candidate prioritization by combining residue scan mutagenesis, predicted binding free energies, and molecular dynamics-based stability assessment.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: actuator
The constructs were designed from the reference peptide UNC10245092 using residue scan methodology, and the top five candidates were selected based on predicted binding free energies. Stability evaluation was performed by molecular dynamics simulation using AMBER, but the supplied evidence does not provide sequence details, expression or synthesis conditions, or delivery strategies.
The available evidence is limited to a single in silico study and reports predicted potency rather than experimental biochemical or cellular validation. No direct measurements of RAF displacement, CIB1 binding affinity, peptide delivery, or activity in triple-negative breast cancer models are provided in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
Approval Evidence
1 source3 linked approval claimsfirst-pass slug designed-decoy-peptides-targeting-cib1
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology. The top five designed peptides (based on binding free energies) were subjected to molecular dynamics simulations using AMBER to evaluate stability.
Source:
comparative bindingsupports
Among the top five selected designed peptides, mutant 2 showed stronger interactions with CIB1 than the reference peptide UNC10245092.
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Source:
design goalsupports
The study aimed to design novel peptides from the reference peptide UNC10245092 to target CIB1 using residue scan methodology.
The goal of this study is to design novel peptides from the reference peptide (UNC10245092) through residue scan methodology.
Source:
predicted mechanismsupports
The selected designed peptides were predicted to have the potency to prevent binding between RAF and CIB1.
and have the potency to prevent the binding of RAF and CIB1.
Source:
Comparisons
Source-backed strengths
The study reports a defined design workflow in which top five peptide variants were selected based on binding free energies and then assessed for stability by molecular dynamics simulation using AMBER. Within this computational set, mutant 2 was reported to interact more strongly with CIB1 than the reference peptide UNC10245092, supporting improved predicted binding.
Source:
Our results indicate that amongst the top five selected peptides, mutant 2 nd mutant have strong interactions with CIB1 than the reference peptide (UNC10245092)
Compared with mMORp
designed decoy peptides targeting CIB1 and mMORp address a similar problem space.
Shared frame: same top-level item type
Strengths here: looks easier to implement in practice.
Compared with self-complementary AAV genomes
designed decoy peptides targeting CIB1 and self-complementary AAV genomes address a similar problem space.
Shared frame: same top-level item type
Compared with split-ring metamaterial sensor with luxuriant gaps
designed decoy peptides targeting CIB1 and split-ring metamaterial sensor with luxuriant gaps address a similar problem space.
Shared frame: same top-level item type
Ranked Citations
- 1.