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Section: New Results

Modeling interfaces and contacts

Keywords: docking, scoring, interfaces, protein complexes, Voronoi diagrams, arrangements of balls.

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

Participants : Frédéric Cazals, Simon Marillet.

In collaboration with Sergei Grudinin, Maria Kadukova and Andreas Eisenbarth (Univ. Grenoble Alpes / CNRS / Inria, France).

The 2015 D3R Grand Challenge provided an opportunity to test our new model for the binding free energy of small molecules [17], as well as to assess our protocol to predict binding poses for protein-ligand complexes. Our pose predictions were ranked 3-9 for the HSP90 dataset, depending on the assessment metric. For the MAP4K dataset the ranks are very dispersed and equal to 2-35, depending on the assessment metric, which does not provide any insight into the accuracy of the method. The main success of our pose prediction protocol was the re-scoring stage using the recently developed Convex-PL potential. We make a thorough analysis of our docking predictions and discuss the effect of the choice of rigid receptor templates, the number of flexible residues in the binding pocket, the binding pocket size, and the subsequent re-scoring.

However, the main challenge was to predict experimentally determined binding affinities for two blind test sets. Our affinity prediction model consisted of two terms, a pairwise-additive enthalpy, and a non pairwise-additive entropy. We trained the free parameters of the model with a regularized regression using affinity and structural data from the PDBBind database. Our model performed very well on the training set, however, failed on the two test sets. We explain the drawback and pitfalls of our model, in particular in terms of relative coverage of the test set by the training set and missed dynamical properties from crystal structures, and discuss different routes to improve it.

Novel structural parameters of Ig-Ag complexes yield a quantitative description of interaction specificity and binding affinity

Participants : Frédéric Cazals, Simon Marillet.

In collaboration with Pierre Boudinot (INRA Jouy-en-Josas) and M-P. Lefranc (University of Montpellier 2).

Antibody-antigen complexes challenge our understanding, as analyses to date failed to unveil the key determinants of binding affinity and interaction specificity. In this work [23], we partially fill this gap based on novel quantitative analyses using two standardized databases, the IMGT/3Dstructure-DB and the structure affinity benchmark.

First, we introduce a statistical analysis of interfaces which enables the classification of ligand types (protein, peptide, chemical; cross-validated classification error of 9.6%), and yield binding affinity predictions of unprecedented accuracy (median absolute error of 0.878 kcal/mol). Second, we exploit the contributions made by CDRs in terms of position at the interface and atomic packing properties to show that in general, VH CDR3 and VL CDR3 make dominant contributions to the binding affinity, a fact also shown to be consistent with the enthalpy - entropy compensation associated with pre-configuration of CDR3. Our work suggests that the affinity prediction problem could be solved from databases of high resolution crystal structures of complexes with known affinity.