NNScore 2.0: a neural-network receptor-ligand scoring function

J Chem Inf Model. 2011 Nov 28;51(11):2897-903. doi: 10.1021/ci2003889. Epub 2011 Nov 3.


NNScore is a neural-network-based scoring function designed to aid the computational identification of small-molecule ligands. While the test cases included in the original NNScore article demonstrated the utility of the program, the application examples were limited. The purpose of the current work is to further confirm that neural-network scoring functions are effective, even when compared to the scoring functions of state-of-the-art docking programs, such as AutoDock, the most commonly cited program, and AutoDock Vina, thought to be two orders of magnitude faster. Aside from providing additional validation of the original NNScore function, we here present a second neural-network scoring function, NNScore 2.0. NNScore 2.0 considers many more binding characteristics when predicting affinity than does the original NNScore. The network output of NNScore 2.0 also differs from that of NNScore 1.0; rather than a binary classification of ligand potency, NNScore 2.0 provides a single estimate of the pK(d). To facilitate use, NNScore 2.0 has been implemented as an open-source python script. A copy can be obtained from http://www.nbcr.net/software/nnscore/ .

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Binding Sites
  • Computational Biology / methods*
  • Databases, Protein
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Ligands
  • Models, Molecular
  • Neural Networks, Computer*
  • Protein Binding
  • Proteins / chemistry*
  • Proteins / metabolism
  • ROC Curve
  • Research Design
  • Software*
  • Static Electricity
  • Thermodynamics


  • Ligands
  • Proteins