Docking@GRID – A Web Portal for Massively Parallel Flexible Docking,

using the ChemAxon toolkit.Dragos Horvath*Dragos Horvath*, Kun Attila, Kun Attila, Benjamin Parent*, , Benjamin Parent*,

Cyrielle BoutroueCyrielle Boutroue##, Even Gaël, Even Gaël##, Alexandru Tantar, Alexandru Tantar##, , Nouredine MelabNouredine Melab##, Sylvaine Roy, Sylvaine Roy & El-Ghazali & El-Ghazali

TalbiTalbi##

* UMR 8576, CNRS – Univ. Lille 1, FR* UMR 8576, CNRS – Univ. Lille 1, FR Chemistry Dept, Univ. Babes-Bolyai, Cluj, ROChemistry Dept, Univ. Babes-Bolyai, Cluj, RO

# LIFL CNRS/INRIA – Univ. Lille 1, FR# LIFL CNRS/INRIA – Univ. Lille 1, FR

DSV/iRTSV - CEA, Grenoble, FRDSV/iRTSV - CEA, Grenoble, FR

Outline…• The goal: automated fully flexible docking on

computer grids – GRID5000, http://www.grid5000.fr

– Specific conformational sampling & docking software based on hybrid genetic algorithms

– Upfront chemoinformatics tools to preprocess submitted ligands.

– Upfront tools to define the active site and its key degrees of freedom (!)

– Interface to start docking calculations & analyze results.

Genetic Algorithm-driven Conformational Sampling Tool

• Based on a Genetic Algorithm, coding conformers as "chromosomes" in which each locus stands for a torsional angle value.

n…

• The In Silico Darwinian Evolution, leading to fitter and fitter (lower energy) conformers, was enhanced by – hybridization with various optimization heuristics

– Fine-tuning of the parameters controlling the evolutionary strategy

Customized CVFF force field, employing:• a 10 Å cutoff (with a termination function)• a smoothing procedure to avoid interatomic clashes• a continuum solvent model

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GRID 5000-based ‘Planetary’ Model

If (free node)DEPLOY

Island Model

- Executables- Molecule File- Constraint Files- Seeds List- Taboo List- Operational Pars

-Stablest Chromosomes-Sampling Success Score

Solution Merger& Clusterer

Conformer & Cluster Database

‘Panspermia’ policy center‘recent’ clusters: seeds

‘old’ clusters: taboo

Sampling Success vs.Operational Pars

Stop:max. ‘Mission Nr.’

no new clusters sinceN ‘missions’

www.grid5000.fr

Operational ParsSelector

• Ab initioAb initio folding of Trp cage 1L2Y: native structure folding of Trp cage 1L2Y: native structure (reproducibly) found and ranked as most stable. (reproducibly) found and ranked as most stable. Planetary model used max. 20 nodes for 4…5 daysPlanetary model used max. 20 nodes for 4…5 days

Conformer # 1, RMS~1.8 Ǻ - good match to native structure

• Ab initioAb initio folding of Trp zipper 1LE1: native structure folding of Trp zipper 1LE1: native structure found and ranked as most stable. Planetary model found and ranked as most stable. Planetary model used max. 20 nodes for 4…5 daysused max. 20 nodes for 4…5 days

Conformer # 1, RMS~0.8 Ǻ - perfect match to native structure

• However, there is a high risk that almost well folded However, there is a high risk that almost well folded solutions, being declared taboo, block the access to solutions, being declared taboo, block the access to the correct fold !!the correct fold !!Conformer # 79, RMS~2.4 Ǻ - near-optimal fold closest to native structureConformer # 1, RMS~3.8 Ǻ - is a poor match of the native structure

Outline…• The goal: automated fully flexible docking on

computer grids – GRID5000, http://www.grid5000.fr

– Specific conformational sampling & docking software based on hybrid genetic algorithms

– Upfront chemoinformatics tools to pre-process submitted ligands.

– Upfront tools to define the active site and its key degrees of freedom (!)

– Interface to start docking calculations & analyze results.

Ligand Preprocessor…

Ligand File

UploadStandardize

Main Tautomer &Key µSpecies

(occurrence > m%)

All Tautomers &Major µSpecies

All Tautomers &Key µSpecies

AddExplicit H

Force FieldTyping

(PMapper)

JChem DataBaseCannonical SMILES

Dockable Conformer Families

Main Tautomer &Major µSpecies

UserToggle

Partial ChargeCalculation

GenerateConformer(s)

If new…

A selector of top N most likely tautomeric forms would be of outstanding help here – many among the enumenated tautomers are chemically meaningless!

Potential problems with resonant structures in the ChargePlugin:

try { ChgPlug.setTakeResonantStructure(true); chgMol=ChgPlug.setMolecule(currSpec,false,false); ChgPlug.run(); …}catch (Exception ResonantStructureFailed) { try { ChgPlug.setTakeResonantStructure(false); … } catch (Exception WhateverYouDoItBreaks) { … }}

Using PMapper to assign CVFF types to ligand atoms

• required SMARTS encoding of the CVFF ‘templates’ corresponding to local neighborhoods defining each potential type

Issues yet to be settled:

• use the Conformer Plugin to generate several hundreds of geometries

Conformer diversity control ? How many degrees of freedom can be handled without significant risk of missing key minima ? Docking will use a different force field – how ‘compatible’ are ConformerPlugin & CVFF energies?

• use the Conformer Plugin to generate a starting geometry, then use a ligand-specific GA-driven sampling engine to explore the phase space.

Outline…• The goal: automated fully flexible docking on

computer grids – GRID5000, http://www.grid5000.fr

– Specific conformational sampling & docking software based on hybrid genetic algorithms

– Upfront chemoinformatics package to pre-process submitted ligands.

– Upfront tools to define the active site and its key degrees of freedom (!)

– Interface to start docking calculations & analyze results.

Active Site Definition…

Ligand..

Fixed protein residuesFixed protein residues

Fixed backbone,Fixed backbone,Mobile sidechainsMobile sidechains

Flexible Loop:Flexible Loop:Backbone (Backbone ( but not but not ) )

& sidechains& sidechains

This part of the backbone is aThis part of the backbone is a« frozen » part of the flexible loop:« frozen » part of the flexible loop:

Rigid body rototranslationsRigid body rototranslations

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Protein Preprocessing Tools…• At this point, the user has to explicitly provide:

– A BioSym .car protein file, with correct protonation states, partial charges and force field types for all protein atoms

– A list of fixed atoms– A list of explicitly ‘broken’ bonds to enable sampling ring

and fixed end loop geometries– A list of active torsional degrees of freedom (otherwise, all

potentially rotatable exocyclic single bonds will be considered)

• Will MarvinSpace evolve such as to allow for graphical input the above-mentioned information?

• Would the Charge Plugin, the MicroSpecies Plugin and PMapper work upon input of a .pdb file?

• JChem Database of defined active sites and their sampled unbound state geometries…

Outline…• The goal: automated fully flexible docking on

computer grids – GRID5000, http://www.grid5000.fr

– Specific conformational sampling & docking software based on hybrid genetic algorithms

– Upfront chemoinformatics tools to pre-process submitted ligands.

– Upfront tools to define the active site and its key degrees of freedom (!)

– Interface to start docking calculations & analyze results.

The Dock Manager• In an ideal world, an academic user may add own

molecule collections to the database, but should be allowed to try docking other people’s molecules as well…– Paranoia Manager: who’s allowed to dock ‘my’ compounds

and use ‘my’ active sites?– Make use of JChem facilities to search ligand database by

cannonical structures, and return all the conformers of associated µSpecies/Tautomers. Chemoinformatic filters welcome, even based on the Holy Rule of Five!

• Methodological progress on the docking algorithms still required:– Is rigid docking of each of ~102 ligand conformers into each

one of the ~104 active site geometries feasible? Would it be assimilable to flexible docking?

– How to score: free energy based on docked vs. unbound ensembles? What about µSpecies & Tautomer penalties?

Docked Conformer Visualization

Conclusions & Perspectives• This is a long-term ANR-funded public research

project: http://dockinggrid.gforge.inria.fr/• The primary goal is developing efficient GRID-based

conformational sampling & docking methodologies– http://paradiseo.gforge.inria.fr/ to provide the core routines

for parallel evolutionary computing

• However, chemically meaningful ligand and active site management is as important as the docking step!– ChemAxon tools for ligand standardizing, protonation,

charge & force field management, 3D-buildup, storage & retrieval, visualizing,…, are perfectly suited!

– Progress needed on macromolecule & active site management. TTHANKSHTHANKSA THANKSNTHANKSKTHANKSS