Developments ‘08…• Inclusion of intermolecular degrees of freedom

• Changes of the genetic algorithm

– Constrained Sampling mini<i≤max

i

– Hybrid Islands, Electrostatic Forcing

– Dynamic Tabus

– Buffered Migrations

• ProCheck structure selection (folding)

• Divide & Conquer “Planetary” strategy

• BestEffort deployment

• Simulation Results

Intermolecular degrees of freedom• Loose fragments detected & considered ligands

• Chromosomes now include real values!– Torsional angles

– 3 Euler angles/ligand

– 3 Translations/ligand

• The site must contain at least one fixed atom.

• Translations (mapped onto [0…359.99], for homogeneity) position the topological center of the ligand within the box occupied by the free atoms of the site – unless a site_def.gen file is provided.

• All Euler angles may evolve between 0 and 360°

n…

One or two islands are allowed to use “heavy” alternative Heuristics.

• At each generation, there is a total (tunable) probability phyb to use “directed” rather than classical mutations:– Torsional driving (Explorers), with a frequency of

(phyb)2 , or – Electrostatic Forcing, with a frequency of phyb(1-

phyb), replacing the ancient time-consuming Monte Carlo simulation.

• Randomy increase weight of electrostatic interactions• Perform gradient relaxation with perturbed Hamiltonian• Reset Hamiltonian and reoptimize

Dynamic Tabus• A geometry is within a tabu zone if, for all degrees of freedom i, the differences i to the declared tabu geometry are below the minimal significant torsional differences si, i.e. max(i /si)<1

• However, making a binary « tabu or not tabu » decision for the current geometry does not suggest any way to escape the tabu zone.

• A smooth & differentiable tabu penalty, decreasing with increasing max(i /si) might permit escaping the tabu area by following the gradients

• A differentialble approximation DMAX(i /si) ≈max(i /si) -1 was defined

• If the energy e of the current geometry falls below the one of the declared tabu structure et, then there is no more interest in leaving the tabu zone – which had been overhastily set!

i

iiis

minmax

t

ii

ee

sDMAXTefitness

exp1

)/(exp

Buffered Migrations• Stalled evolution of an island triggers population reset

(apocalypse) in order to let the sampler move to other phase space zones.

• If a migrant– likely related to the ancient population – enters the island, it will be fittest among primitive post-reset individuals– It will have a lot of children and drive natives to extinction

• Strategy change: incoming migrants enter a buffer zone* and are released into the population as soon as its evolutionary dynamics seems to slow down– After 20 successive generations without progress, an island

“opens” to migrants (in the mean time, natives should be comparable to migrants – if not, they deserve extinction)

* Hortefeux, B., Sarkozy, N., “L”Immigration Choisie”, pp. 1-29 in The Alien Menace, Le Pen, J.M. Ed., Vichy Press (2007)

ProCheck used to discard misfolded protein conformers…

Discard Structure if:

• Has more than one residue in forbidded Rama-chandran area• Has a goodness factor < -1.0• Has no minimal contigouos sequence of secondary structure elements (AAA or BBB.*BBB)

Torsions of residues outside core regions are discarded from the list of preferential values in seeding

Divide-and-Conquer Planetary Strategy

• Allocates a number of nodes to be used for global (NG) and local (NL) sampling.

• Global searches return a set of diverse low-energy conformers, representing potentially interesting cells.

• Once such cells were found and stored into the Open Cell Repository (OCR) they are eligible for local sampling.

• After the fifth local search, a cell will be closed (added to the Closed Cell Repository CCR) if the current run failed to discover any more stable geometry.

Dispatcher

Detect Running Jobs

G

LrunningG

runningL

N

N

N

N

Submit Global Search

• Set WALLTIME• Select SEED and TABU from CCR (if enough entries)• Select Operational parameters.

Submit Local Search

• Set WALLTIME/• Pick a cell from OCR• Use ICR as SEED

Detect Result Type

Closed Cell

• Add to CCR

Open Cell

• Add to OCR• Add geometries to ICR

Global Search

• Assign found geo-metries to cells• Merge entries into OCR (keep stablest geometry /cell)• Update Sampling success vs. Opera-tional pars. table

Launching ModeResult Integration Mode

BestEffort Deployment• The scheduler now runs on a regularly reserved

node, no longer on the frontend machine.– It checks for the list of currently deployed besteffort nodes

and decides upon jobs to be assigned to each of these.– The panspermia strategy – selecting seeds and tabus –

and the selection of the next cell to be submitted to local sampling – based on energy & diversity criteria – may now be performed without risking to overload the frontend machine

• BestEffort nodes are running waiting loops, expecting a job assignment file (global or local search, tabus, seeds, cell to explore, etc.).

• The frontend runs a meta-scheduler checking, every 2 minutes, the state of the nodes, and trying to restart terminated tasks.

Conclusions & Perspectives• The divide-and-conquer planetary strategy apparently works

better than any other before– 1L2Y folded in <24 h, several days were needed before– However, there are no resources to lead any decent benchmarking

concerning the choice of Kmax, NG/NL, etc. – It is practically out of question to use GRID 5000 for docking

experiments on various systems!!• BestEffort deployment sucks!

– Having jobs killed is not the worst thing that may happen– Having the one regular reservation (for the node running the scheduler)

postponed lets all the other nodes do… nothing in BestEffort mode – they run an empty loop waiting for jobs no one submits!

– Cannot run the scheduler in besteffort – getting it killed while accessing result databases may corrupt everything

• We need some dedicated 100 nodes in order to make real progress.

• Ab initio folding of Trp cage 1L2YTrp cage 1L2Y: native structure (reproducibly) found and ranked as most stable. Planetary model used max. 20 nodes for 4…5 days

PDB PDB

• Ab initio folding of the Villin headpiece 1VIIVillin headpiece 1VII: helical parts are seen to fold in a matter of days (40 nodes) – although not properly oriented.

PDB PDB

• Good news for the -hairpin of ChignolinChignolin: out of the top 10 best ranked conformers, 8 are native-like

• Number one is not – but in this case, that may not be a problem

PDB PDB

#1,#5#1,#5

• However, proper folding of 1LE1 could be achieved (though not reproducibly!) with previous force field versions – is the current setup too helix-specific?

• The Trp Zipper 1LE1 Trp Zipper 1LE1 -sheet is not the absolute energy minimum according to the current setup!

PDB PDB

• Docking simulations in presence of flexible loops, such as the hinge region of Casein Kinase 2 (3BQC)Casein Kinase 2 (3BQC)

– pose of ligand emodin and loop geometry are correctly predicted (3BQC not in FF training set).

PDB, #1

PDB, #1

Conclusion, Status &Needs…

• We have working sampling & docking software, which must now be – Fine tuned– Helped to reduce the scope of search, by exploiting

experimental (preferred rotamers, etc) or empirical knowledge (required key interactions, fingerprints, etc)

– Also exploited in other 3D chemoinformatics approaches, with higher throughput than docking

• Need our own CLUSTER (~100 nodes or mode)– Invest in existing platforms for privileged access– Buy own (with system manager)– One postdoc