1 / 21

Meshi – a new object oriented package for molecular simulations

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.

giolla
Download Presentation

Meshi – a new object oriented package for molecular simulations

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 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

  2. Challenges of computational structural biology • Computational determination of biomolecular structures. • Simulation of biomolecular dynamics. • Molecular design.

  3. Computational tasks • Represent the system. • molecular level? • monomer (residue, nucleotide etc. ) level? • Atom level? • All levels? • Measure structural properties.

  4. Computational tasks (cont.) • Evaluate structures • Move from one structure to another.

  5. Why a new package ? • Why Java ?

  6. The modular, object oriented approach of Meshi. Sample classes

  7. Coordinates Coordinates X Y Z Forces FX FY FZ

  8. Atom coordinates name type

  9. atom1 atom2 Distance update

  10. 1 2 4 5 3 DistanceMatrix 1 2 3 4 5 6 update

  11. Angle update

  12. AngleEnergyElement Atom type specific constants 1.Evaluate 2.Update atom forces

  13. AngleEnergy A list of elements 1.Evaluate 2.Update atom forces

  14. TotalEnergy 1.Update DistanceMatrix 2.Evaluate 3.Update atom forces

  15. 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.

  16. H O O H 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.

  17. 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. H O O H

  18. 1NXJ – T0156 Shotgun 12.5Å (7.4) Shotgun beautified 11.1Å (6.5(Å native

  19. Package Tree filters Filter util MeshiList meshi molecularElements Atom Atomlist AtomPair AtomPairList Residue ResidueList Protein geometry Distance DistanceMatrix Angle Torsion energy AbstractEnergy TotalEnergy EnergyElement EnergyCreator Parameters ParametersList. optimizers SteepestDecent LBFGS ca CaProtein backbone BackboneProtein bond BondEnergy BondEnergyElement BondParameters BondParametersList BondCreator angle AngleEnergy AngleEnergyElement AngleParameters AngleParametersList AngleCreator residuesUnitedAtoms UnitedAtomsResidue Ala Cys Asp Glue….

  20. PDB file format PFRMAT TS TARGET T0201 AUTHOR 3594-1086-1033 METHOD Ab-initio with Mshi potential. ATOM 0 N MET 1 0.435 18.047 15.636 1.00 1.00 ATOM 1 CA MET 1 -0.348 19.275 15.891 1.00 1.00 ATOM 4 CB MET 1 -1.750 18.918 16.383 1.00 1.00 ATOM 2 C MET 1 0.311 20.164 16.940 1.00 1.00 ATOM 3 O MET 1 1.325 20.822 16.675 1.00 1.00 ATOM 5 CG MET 1 -1.743 18.524 17.850 1.00 1.00 ATOM 6 SD MET 1 -0.926 16.937 18.135 1.00 1.00 ATOM 7 CE MET 1 -2.309 15.850 17.843 1.00 1.00 ATOM 8 H ILE 2 -1.230 19.859 18.093 1.00 1.00 ATOM 9 N ILE 2 -0.367 20.225 18.087 1.00 1.00 ATOM 10 CA ILE 2 0.093 20.893 19.300 1.00 1.00 ATOM 13 CB ILE 2 -0.961 21.864 19.867 1.00 1.00 ATOM 11 C ILE 2 0.283 19.938 20.469 1.00 1.00 ATOM 12 O ILE 2 -0.433 18.948 20.610 1.00 1.00 ATOM 14 CG1 ILE 2 -2.157 21.058 20.375 1.00 1.00 ATOM 15 CD1 ILE 2 -1.776 20.107 21.497 1.00 1.00 ATOM 16 CG2 ILE 2 -1.417 22.904 18.851 1.00 1.00

  21. A sample commands file MinimizeProtein.prm parameters /users/faculty/cs/keasar/progs/meshi/current/meshi/parameters bondEnergy weight 1 LennardJones weight 1 angleEnergy weight 1 planeEnergy weight 1 outOfPlaneEnergy weight 1000 minimize tolerance 0.01 minimize maxSteps 500 minimize reportEvery 10

More Related