Source 1primary paper2013Biochemistry
Toolkit/all-atom replica exchange discrete molecular dynamics
all-atom replica exchange discrete molecular dynamics
Also known as: docking models generated by all-atom replica exchange discrete molecular dynamics
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
All-atom replica exchange discrete molecular dynamics is a computational docking method used to generate structural models of calcium and integrin binding protein 1 (CIB1) bound to α-integrin cytoplasmic tails. In the cited CIB1 study, it predicted that multiple α-integrin tails engage the same hydrophobic binding pocket on CIB1.
Usefulness & Problems
Why this is useful
This method is useful for proposing structural models of protein-peptide binding when direct complex structures are not provided in the cited evidence. In the CIB1 system, it supported interpretation of how several α-integrin cytoplasmic tails could recognize a common hydrophobic site and helped contextualize competitive binding observations.
Problem solved
It addresses the problem of inferring the binding mode of multiple α-integrin cytoplasmic tails to CIB1. Specifically, it was used to predict whether distinct α-integrin tails could dock to the same hydrophobic pocket on CIB1.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
recombinationImplementation Constraints
The evidence identifies the approach only as 'docking models generated by all-atom replica exchange discrete molecular dynamics.' No details are provided on software, force field, replica number, temperature ladder, input structure preparation, or required computational resources.
The supplied evidence only supports its use as a computational docking approach in the CIB1–α-integrin context and does not report broader benchmarking, accuracy metrics, or prospective validation. No implementation performance details, generalizability data, or independent replication beyond the cited study are provided.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2020UNC Libraries
Ranked Claims
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Binding between CIB1 and α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays showing that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site on αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site on αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
CIB1 binding to α-integrin cytoplasmic tails is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Isothermal titration calorimetry measurements indicated that this binding is driven by hydrophobic interactions and depends on residues in the CIB1 consensus binding site.
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Key residues in the CIB1 binding site of αIIb are well conserved across α-integrin cytoplasmic tails, enabling delineation of a consensus binding site I/L-x-x-x-L/M-W/Y-K-x-G-F-F.
A sequence alignment of all α-integrin CTs revealed that key residues in the CIB1 binding site of αIIb are well-conserved, and was used to delineate a consensus binding site (I/L-x-x-x-L/M-W/Y-K-x-G-F-F).
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Other α-integrin cytoplasmic tails compete with the αIIb cytoplasmic tail for binding to CIB1 in vitro.
solid-phase competitive binding assays, which showed that other α-integrin CTs compete with the αIIb CT for binding to CIB1 in vitro
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Approval Evidence
2 sources2 linked approval claimsfirst-pass slug all-atom-replica-exchange-discrete-molecular-dynamics
docking models generated by all-atom replica exchange discrete molecular dynamics
Source:
docking models generated by all-atom replica exchange discrete molecular dynamics
Source:
computational binding predictionsupports
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Source:
computational binding predictionsupports
Docking models predicted that multiple α-integrin cytoplasmic tails can bind the same hydrophobic binding pocket on CIB1.
We predicted that multiple α-integrin CTs were capable of binding to the same hydrophobic binding pocket on CIB1 with docking models generated by all-atom replica exchange discrete molecular dynamics.
Source:
Comparisons
Source-backed strengths
The method produced docking models that converged on a shared hydrophobic binding pocket on CIB1 for multiple α-integrin cytoplasmic tails. This prediction is consistent with reported hydrophobic interaction dependence and with in vitro competition among α-integrin tails for CIB1 binding.
Ranked Citations
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