Meshi – a new object oriented package for molecular simulations

Nir Kalisman, Ami Levi, Sharon Zafriri-lynn, Ram Janovski and Chen Keasar

Departments of Computer Science and Life Sciences BGU

Challenges of computational structural biology

Computational determination of biomolecular structures.

Simulation of biomolecular dynamics.

Molecular design.

Computational tasks

Represent the system.molecular level?monomer (residue, nucleotide etc. ) level?

Atom level? All levels?

Measure structural properties.

Computational tasks (cont.)

• Evaluate structures

• Move from one structure to another.

Why a new package ?

Why Java ?

The modular, object oriented approach of Meshi.

Sample classes

Coordinates

CoordinatesX Y Z

ForcesFX FY FZ

Atom

type

name

coordinates

Distance

Z

d

Y

d

X

d

d

1atom1 atom2

d2

update

d

1

2

3

4

5

6

1 2 3 4 5

DistanceMatrix

update

Angle

ZYX

update

AngleEnergyElement

K

Atom type specific

constants

1.Evaluate

2.Update atom forces

2

Ke

AngleEnergy

1.Evaluate2.Update atom forces

A list of elements

eEangle

TotalEnergy

1.Update DistanceMatrix2.Evaluate

3.Update atom forces

term

termtotal eE

LBFGS(minimizer)

A list of coordinates

1.Update energy and forces

2.Change the coordinated

according to the forces.

3.If not yet in a minimum -

go to 1.

Current Meshi projects

Novel algorithm for non-bonded-list

generation.

MCMM-like stochastic optimization.

Continues knowledge-based potential for

pairs of torsion angles.

Cooperative hydrogen-bonds potential.

A refinement program for fold-recognition

models.

HO O

H

Novel algorithm for non-bonded-list

generation.

MCMM-like stochastic optimization.

Continues knowledge-based potential for

pairs of torsion angles.

Cooperative hydrogen-bonds potential.

A refinement program for fold-recognition

models.

HO O

H

1NXJ – T0156

native

Shotgun12.5Å (7.4)

Shotgun beautified11.1Å (6.5(Å

Package Tree

meshi

molecularElementsAtom Atomlist AtomPair AtomPairListResidue ResidueListProtein

geometryDistance DistanceMatrixAngleTorsion

energyAbstractEnergyTotalEnergyEnergyElementEnergyCreatorParametersParametersList.

optimizersSteepestDecentLBFGS

caCaProtein

backboneBackboneProtein

residuesUnitedAtomsUnitedAtomsResidueAla Cys Asp Glue….

bondBondEnergyBondEnergyElementBondParametersBondParametersListBondCreator

angleAngleEnergyAngleEnergyElementAngleParametersAngleParametersListAngleCreator

utilMeshiList

filtersFilter

PDB file format

PFRMAT TSTARGET T0201AUTHOR 3594-1086-1033METHOD Ab-initio with Mshi potential.ATOM 0 N MET 1 0.435 18.047 15.636 1.00 1.00ATOM 1 CA MET 1 -0.348 19.275 15.891 1.00 1.00ATOM 4 CB MET 1 -1.750 18.918 16.383 1.00 1.00ATOM 2 C MET 1 0.311 20.164 16.940 1.00 1.00ATOM 3 O MET 1 1.325 20.822 16.675 1.00 1.00ATOM 5 CG MET 1 -1.743 18.524 17.850 1.00 1.00ATOM 6 SD MET 1 -0.926 16.937 18.135 1.00 1.00ATOM 7 CE MET 1 -2.309 15.850 17.843 1.00 1.00ATOM 8 H ILE 2 -1.230 19.859 18.093 1.00 1.00ATOM 9 N ILE 2 -0.367 20.225 18.087 1.00 1.00ATOM 10 CA ILE 2 0.093 20.893 19.300 1.00 1.00ATOM 13 CB ILE 2 -0.961 21.864 19.867 1.00 1.00ATOM 11 C ILE 2 0.283 19.938 20.469 1.00 1.00ATOM 12 O ILE 2 -0.433 18.948 20.610 1.00 1.00ATOM 14 CG1 ILE 2 -2.157 21.058 20.375 1.00 1.00ATOM 15 CD1 ILE 2 -1.776 20.107 21.497 1.00 1.00ATOM 16 CG2 ILE 2 -1.417 22.904 18.851 1.00 1.00

parameters /users/faculty/cs/keasar/progs/meshi/current/meshi/parameters

bondEnergy weight 1LennardJones weight 1angleEnergy weight 1planeEnergy weight 1outOfPlaneEnergy weight 1000

minimize tolerance 0.01minimize maxSteps 500minimize reportEvery 10

A sample commands fileMinimizeProtein.prm