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Soft Matter Physics

RBind
RBind:computational network method to predict RNA binding sites.

HKPocket
HKPocket:Human kinase pocket database for drug design.

RPocket
RPocket:RNA pocket database for drug design.

RPpocket
RPpocket:RNA pocket database for RNA-protein interaction and drug design.

Molecular Structure Resources

• PDB - protein 3D structuredatabase 


• SCOP- Structural Classification Of Proteins 


• NDB 

Sequence Alignment

• MAFFT (≤ 500 sequences) 


• MUSCLE (≤ 500 sequences) 


• T-Coffee (≤ 500 sequences) 


• Kalign (≤ 2000 sequences) 


• Clustal Omega (≤ 4000 sequences) 

Molecular Modeling

• I-TASSER 


• MODELLER 


• SWISS-MODEL 


• 3dRNA 

Molecular Dynamics

• AMBER 


• CHARMM 


• Gromacs 

Molecular Docking

• DOCK 


• ZDOCK 


• AutoDock 

Molecular Visualization/Analysis

• PyMol 


• Chimera 


• VMD