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Example of AD-ENM: myosin
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In this example, we study the conformational changes in dicty myosin from the transition state (PDB code: 1VOM) to the near-rigor
state (PDB code: 1MMA), where the local structural deformation occurs at the nucleotide-binding pocket.
For Option 1, upload the following two PDB files as input:
The first PDB file is 1VOM.
The second PDB file is 1MMA.
For results click here.
For Option 2, upload the following two PDB files as input:
The first PDB file is 1VOM.
The second PDB file is new pocket conformation.
For results click here.
For Option 3, upload the following two PDB files as input:
The first PDB file is 1VOM.
The second PDB file is pocket residues.
For results click here.
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Example of DC-ENM
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In this example, we are given the 1st PDB structure 1OMP and a data file with 2 DCs, and we wish to model a new structure that satisfies the given DCs. You can submit the above two files here, together with the 2nd PDB structure 1ANF which is the native structure we try to model. DC-ENM will then generate a structural model and compare it with the 2nd PDB structure.
The results of running DC-ENM with the above example are shown here.
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Example of PATH-ENM
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In this example of myosin structural transition, we wish to map the transition path from the 1st PDB structure 1VOM to the 2nd PDB structure 1MMA. You can submit the above two files here. PATH-ENM will then generate two transition paths (SD path and SP path).
The results of running PATH-ENM with the above example are shown here.
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Example of iENM
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In this example of myosin structural transition, we wish to map the transition path from the 1st PDB structure 1VOM to the 2nd PDB structure 1MMA. You can submit the above two files here. iENM will then generate a transition path.
The results of running iENM with the above example are shown here.
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Example of EMFF
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In this example, we flexibly fit an initial structure of adenylate kinase given by the 1st PDB structure 1AKE into a simulated EM map (X-PLOR format, 10Å resolution) based on the 2nd PDB structure 4AKE. You can submit the above three files here.
The results of running EMFF with the above example are shown here.
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