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John Mitchell; James McDonagh ; Neetika Nath. Rob Lowe; Richard Marchese Robinson . RF-Score: a Machine Learning Scoring Function for Protein-Ligand Binding Affinities . Ballester, P.J. & Mitchell, J.B.O. (2010) Bioinformatics 26, 1169-1175 .

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John Mitchell; James McDonagh; NeetikaNath

Rob Lowe; Richard Marchese Robinson


Rf score a machine learning scoring function for protein ligand binding affinities
RF-Score: a Machine Learning Scoring Functionfor Protein-Ligand Binding Affinities

  • Ballester, P.J. & Mitchell, J.B.O. (2010) Bioinformatics 26, 1169-1175




Three existing approaches …

2. Empirical Functions


Three existing approaches …

2. Empirical Functions


Three existing approaches …

3. Knowledge based





We thought about this … being independent.

… and wrote a paper saying

“It’s not true, but it sort of works”


We thought about this … being independent.

… and wrote a paper saying

“It’s not true, but it sort of works”




  • And persuade someone to pay for it!


Random Forest distribution to the binding free energy …

Predicted binding affinity


Random forest
Random Forest distribution to the binding free energy …

● Introduced by Briemann and Cutler (2001)

● Development of Decision Trees (Recursive Partitioning):

● Dataset is partitioned into consecutively smaller subsets

● Each partition is based upon the value of one descriptor

● The descriptor used at each split is

selected so as to optimise splitting

● Bootstrap sample of N objects chosen from the N available objects with replacement


distribution to the binding free energy …The Random Forest is a just forest of randomly generated decision trees …

… whose outputs are averaged to give the final prediction


Building rf score
Building RF-Score distribution to the binding free energy …

PDBbind 2007


Building rf score1
Building RF-Score distribution to the binding free energy …

PDBbind 2007


Validation results pdbbind set
Validation results: PDBbind distribution to the binding free energy …set

 Following method of Cheng et al. JCIM 49, 1079 (2009)

 Independent test set PDBbind core 2007, 195 complexes from 65 clusters


Validation results pdbbind set1
Validation results: PDBbind distribution to the binding free energy …set

  • RF-Score outperforms competitor scoring functions, at least on our test

  • RF-Score is available for free from our group website


John Mitchell; James distribution to the binding free energy …McDonagh; NeetikaNath

Rob Lowe; Richard Marchese Robinson


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