TopoDesign

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Load demo input files and arguments
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Input PDB file
Upload the protein structure file in PDB format.
Input sequence
Paste a sequence or upload a
sequence file in FASTA format
if there is no known structure
information. Structure will be
predicted by ESMFold firstly.
Length of amino acids should
lower than 500.
Parameters
*Design mode
Design model refers to how a program handles multi-chain input files. “Singledomain” means that all chains are connected sequentially into one chain and then creating topological variants based on the single-chain input. “Mupltidomain” model is under development.
Select the Topology model firs
This parameter means how
the program deal with
multi-chain situations.
Currently, the program
only apply for single-domain
topological protein design.
*Number of split loops
Design model refers to how a program handles multi-chain input files. “Singledomain” means that all chains are connected sequentially into one chain and then creating topological variants based on the single-chain input. “Mupltidomain” model is under development.
Select the Topology model firs
This parameter means the
number of loops will be splitted
from the input PDB file.
The lower the number of
split loops, the higher the
success rate of the design.
Use sequence design
Design model refers to how a program handles multi-chain input files. “Singledomain” means that all chains are connected sequentially into one chain and then creating topological variants based on the single-chain input. “Mupltidomain” model is under development.
Fast TopoDesign will not
consider the sequence of
rewiring loops. It costs
less time and gives a
determined connection.
If you use sequence design,
the program will generate
a optimezed sequence result.
*Topology mode
Design model refers to how a program handles multi-chain input files. “Singledomain” means that all chains are connected sequentially into one chain and then creating topological variants based on the single-chain input. “Mupltidomain” model is under development.
Select the Topology model firs
The connected relationship
will be different when different
topology mode is selected.
Specified topology types
Design model refers to how a program handles multi-chain input files. “Singledomain” means that all chains are connected sequentially into one chain and then creating topological variants based on the single-chain input. “Mupltidomain” model is under development.
  • Hopf Link
  • Solomon Link
  • Star of David
  • 3_1 Knot
  • 4_1 Knot
  • 5_1 Knot
  • 5_2 Knot
    • Confirm
If you are particularly interested
in certain topological structures,
you can select them here. The
program will selectively give
the corresponding results.
Selected chains
You can specify a chain for
design. If not specified, the
program will automatically
recognize the first chain
in the file for design.
Restraint residues
You can specify some residues
that can not be disturbed.
Those loops contained the
residues will not be splitted
during thedesign process.
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