This document discusses molecular docking using multiple receptor conformations (MRC) to address receptor flexibility, one of the major challenges in docking. It notes that while ligand flexibility has been addressed, receptor flexibility remains difficult. The document outlines different approaches to incorporate receptor flexibility in docking and explains that MRC docking uses multiple predetermined receptor structures to represent flexibility. However, it also warns that too many MRCs could increase false positives in virtual screening. The key to successful MRC docking is using a representative set of binding site conformations without unnecessary artifact structures.

1. MRC DOCKING
KRITIKA DHIMAN
AKHIL DINESAN
AJIT KUMAR SINGH
(MSC BIOINFORMATICS)

2. INTRODUCTION
 Molecular docking is playing an important role in lead discovery and design.
 Yet it is far from the goal of accurately and reliably predicting complex structures for arbitrary ligand-
receptor interactions.
 And current prediction models are inadequate to for accurate docking prediction.
 Ligand flexibility has been addressed till some extent but receptor flexibility remains a formidable
challenges.
 Diversity in ligand binding mechanisms and the frequent unpredictability of receptor movement types
makes the use of pre-determined multiple receptor conformations(MRC) an attractive practical
alternative.

3.  Approaches to incorporate receptor flexibility in ligand docking :
a) ‘soft’ receptors that limit penalties due to steric clashes
b) selection of a few critical degrees of freedom in the binding site
c) use of multiple receptor structures
d) use of modified molecular simulation methods
e) use of collective degrees of freedom as a new basis of representation for protein flexibility
 A binding site typically consists of 10-20 amino acids side chain, which means dozen of possible torsion
angles.
 Receptor flexibility incorporation into docking simulations must restrict radically the subspace of the full
protein conformational space that they actually search.

4. PROBLEMS BEYOND RECEPTOR
FLEXIBILITY
 It includes incorrect position of ligand pocket atoms, incorrect orientation of His, Arg
and Gln side chains, incorrect tautomer of Histidine and and charged states of
Asparate, glutamate and histidine.
 These inevitable receptor ambiguities effect the MRC methods in two ways:
I. First, we need to take those possibilities into account upon adding any protein
structure to the MRC set.
II. Second, as an added benefit, the multiple receptor structures may represent those
uncertainties in specific atomic details of the receptor binding pocket, including
alternative tautomer, isomers, ring puckering, protonation states, hydrogen positions
and presence/absence of specific water molecules.

5. MULTIPLE RECEPTOR CONFORMATIONS
AND VIRTUAL SCREENING
 While MRC docking may improve pose prediction, each additional conformation
increases the chance of a false positive in VLS.
 Possible increases in false positive rates with the number of MRCs are also
encountered in protein-protein docking simulations.
 Success of MRC docking approach critically depends on two aspects:
I. Firstly, the set should ideally be representative of all or most of the binding site
conformations realized in nature.
II. Secondly, it is equally important to avoid artifact conformations which can result
in both, incorrect pose prediction and false positives in virtual screening.

6. CONCLUSION
 MRC approach is relatively fast and still suitable
for virtual ligand screening as long as the
number of fixed receptor conformations is
relatively small and carefully chosen.