TopologyNet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TopologyNet

Tool usage distribution map

This map represents all the scientific publications referring to TopologyNet per scientific context
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Associated diseases


Popular tool citations

chevron_left Protein-ligand docking Binding affinity prediction Stability change prediction chevron_right
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TopologyNet specifications


Unique identifier OMICS_19937
Name TopologyNet
Interface Web user interface
Restrictions to use None
Input data For Soluble protein ddG: Input Protein, Chain ID, Residue, Wild Name, Mutant, Experimental pH. For Protein-ligand binding affinity: The 3D structures of protein and ligand in bound position.
Input format PDB, mol2
Computer skills Basic
Stability Beta
Maintained Yes


  • person_outline Guowei Wei

Publication for TopologyNet

TopologyNet citation


Opportunities and obstacles for deep learning in biology and medicine

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] quences [,].Structure-based deep learning methods differ in whether they use experimentally derived or predicted ligand–target complexes and how they represent the 3D structure. The Atomic CNN [] and TopologyNet [] models take 3D structures from PDBBind [] as input, ensuring the ligand–target complexes are reliable. AtomNet [] samples multiple ligand poses within the target binding site, and DeepV […]

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TopologyNet institution(s)
Department of Mathematics, Michigan State University, East Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA
TopologyNet funding source(s)
Supported by National Science Foundation IIS-1302285, National Science Foundation DMS-1721024 and Michigan State University.

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