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DCD data is being uploaded
Network Analysis of Protein Structures
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Status:
Trajectory data is being uploaded
Protein
Protein Complex
MD Trajectory
RNA
Network Parameters
EXAMPLE
Analysis Type :
Ensemble Analysis
Timestep Analysis
Network Type :
Energy Network
C-alpha
C-beta
Dynamic Cross correlation network
Weight:
Weighted
Unweighted
Low threshold:
High threshold:
Percent threshold: (%)
MD Parameters
Force Field Type :
Charmm
Amber
Start timestep:
End timestep:
Stride:
PDB File:
Trajectory File(DCD) :
Submit
PDB :
or
File :
Eg: Protein chain
Eg: Protein-Protein
Eg: Protein-DNA
Eg: Protein-RNA
Eg: RNA
Complex Type :
Protein complex
Protein-DNA complex
Protein-RNA complex
No. of Chains :
Two chains
Three chains
Four chains
Chain 1:
Chain 2:
Chain 3:
Chain 4:
Network Type :
C-alpha
C-beta
Atom pair contact
Centroid
Interaction strength
Energy network
Force Field Type :
Charmm
Amber
Weight :
Unweighted
Weighted
Lower threshold (Å) :
Upper threshold (Å) :
Residue separation:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Submit
Related publications:
1) Chakrabarty B and Parekh N,
NAPS: Network Analysis of Protein Structures
,
Nucleic Acids Res.
,
44(W1)
, W375-82, (2016)
2) Chakrabarty B, Naganathan V, Garg K, Agarwal Y and Parekh N,
NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes
,
Nucleic Acids Res.
47(W1)
, W462–70, (2019)
