Monthly Report

August 2004

• starting at EML Research
• making the PhD-exam (3 days in Munich)
• getting to know the infrastructure of EML (ID card, computer account, telefon,...)
• getting on overview of the new literature
• checking protonation state and hydrogens of given pdb files
• converting pdb files for using in amber (C++ programm)
• creating a concept for putting the data into mysql
• installation of mysql on priamos (together with Jan)

September 2004

• putting programs for converting pdb files into bash-script for running automatic procedure
• problems with assigning atom types of ligand with antechamber
• setting new parameters for lead component of the investigated ligand.
• trying different restraints for minimization in sander
• figure for a review

October 2004

• figure for a review (pdf, 4.6 MB)
• first Combine analysis
• 3-months-report (28.10.2004)
• telephone conference (28.10.2004)
  

November 2004

• conference at EMBL "Structures in Biology"
• GDCh - 18. CIC-Workshop in Boppard
• preparing data set of structures of uPA for COMBINE anlaysis
• starting cooperation with Olga Krebs (EML Research, Scientific Databases and Visualization) for designing of database for protein-ligand interaction complexes (first concept)
  
• removing some bugs of the programs for preparing pdb files

December 2004

• writing program for calculating interactions with anal (amber7)
  
• preparing data set of structures of uPA for COMBINE anlaysis
• learning GOLPE
  
• Combine analysis on 31 uPA structures (uro1)
  
• modification of programs for reading various pdb-files without hydrogens
• problem of adding hydrogens to small molecules
• christmas holidays

January 2005

• implementation of adding hydrogens to the protein and ligand by WHATIF and insightII, respectively
• problems of assigning atom types with antechamber
• 6-months-report

February 2005

• building new urokinase model
  
• preparing visit at AstraZeneca
• visit at AstraZeneca (19.-25. Febr. 05)
• problems of assigning parameters with antechamber are solved by using SDF files
• bug fix in some of the scripts and programs
  

March 2005

• Creating SDF files with all important entries (ID, residue, netcharge, PDB).
• Compare minimizations of 1o5a (1o5a.min.tar.gz)and 1o5c (1o5c.min.tar.gz) with different protonation states and restrains. For next COMBINE models structures with HID57 and phenolOH will be used.
  
36 structures of urokinase were aligned with pymol to structure 1o5a.pdb (uPA.align.pdb.tar.gz) and the different sidechain conformations in the active site were compared (superposition of different uPA structures, compare_target.tif). Three important alternative conformations could be found (His99, Gln192, Arg217).

general template: 1o5a
His99: A (not uniform conformation), template: 1sqt; B (more likely than A), template: 1o3p
Gln192: A, template: 1c5z; B (prossibly mixture of conformation A and C), template: 1gi8; C, template 1o3p
Arg217: A (not or very week defined in the available electron density maps), template: 1c5z; B (well defined), template: 1owd

Models were changed:
ALA190 changed to SER190 with conformation from 1o3p.



1o5a
model (uPA-models.tar.gz)	His99	Gln192	Arg217
1 (model1.pdb)	A (1sqt)	A (1c5z)	B (1owd)
2 (model2.pdb)	B (1o3p)	A (1c5z)	B (1owd)
3 (model3.pdb)	A (1sqt)	B (1gi8)	B (1owd)
4 (model4.pdb)	B (1o3p)	B (1gi8)	B (1owd)
5 (model5.pdb)	A (1sqt)	C (1o3p)	B (1owd)
6 (model6.pdb)	B (1o3p)	C (1o3p)	B (1owd)

The six models were in sander by 50 steps (restrain: mainchain 500, sidechain 50, residue H99/Q192/R217 1).
(uPA xray structures and their alternative conformations)
selected water molecules


• Change the programs convert.sh and xleap.sh for running via command line.
• Table with residue names, netcharges, Ki,... (table)
  

April 2005

• Selection of important water molecules for ligand binding in uPA.
• Assigning parameters with antechamber.
• 9-month-report
• Poster for "19th Darmstadt Molecular Modelling Workshop in Erlangen"

May 2005

• "19th Darmstadt Molecular Modelling Workshop in Erlangen" (3.-4.5.2005) (poster)
  
• preparation of files for visit in Mlndal
  

June 2005

• vacation 26th May - 19th June
  
• visit in Mlndal 31st May - 1st June
• docking of ligand of 1ghw into active site of model1
  
• Cluster Analysis of water sites of urokinase-ligand-complexes
• EML lab report
  

July 2005

• adapting changes made in Mlndal to the programs and scripts
  
• testing various minimization protocols with different dielectric constants (docking)
• learning more about GOLD and other docking methods
• learning CORINA
  
• paper review

August 2005

• preparation and correction of SD file (all_300805_3D.sdf, PDB_uPA_300805_3D.sdf)
  
• docking experiments in GOLD (PDF) (still in process!)
  

September 2005

• visualization of molecular interactions (red =-1, white, blue 1; model5-elec-surface.png, model5-elec-surface-ligands.png, model5-vdw-surface.png, model5-vdw-surface-ligands.png, model5-vdw.avi, model5-elec.avi)
  
• new COMBINE models
• new COMBINE model with strong constraints on minimized training set
• Results of new COMBINE models

October 2005

• various COMBINE models for urokinase together with docking results
• 15-month-report (word)

November 2005

• building urokinase COMBINE models (problems with outliers based on wrong Ki values)1 2*
  
• correcting Ki values
• optimizing UHBD protocol
• analysing UHBD solvation energy terms
• building new urokinase COMBINE models with changed Ki values*
  
• testing for outliers*
  
• urokinase COMBINE model (excel file): various models tested with re-docked ligands (with changed Ki values and solvation energy terms)*
  
• annual report
  
• 1^st German Conference on Chemoinformatics / 19. CIC-Workshop (13. - 15. November 2005, Goslar)
• Medientraining
  

December 2005

• German Biotech-Industrie goes Wertschpfung (1.12.2005, Industriepark Hchst)