Krzysztof Rataj, MSc

Krzysztof Rataj, MSc

 

e-mail: rataj@if-pan.krakow.pl
phone: +4812 66 23 301

 

 

 Research interests:

  • computer-aided drug design
  • pharmacophore modeling
  • virtual screening
  • machine learning
  • homology modelling

Publications:

  1.  Witek, J.; Smusz, S.; Rataj, K.; Mordalski, S.; Bojarski, A. J. An application of machine learning methods to structural interaction fingerprints–a case study of kinase inhibitors. Bioorg. Med. Chem. Lett.  201424, 580-585 (http://www.ncbi.nlm.nih.gov/pubmed/24374279)
  2. Rataj, K.; Witek, J.; Mordalski, S.; Kosciolek, T.; Bojarski, A. J. Impact of template choice on homology model efficiency in virtual screening. J. Chem. Inf. Model. 201454, 1661-1668 (http://www.ncbi.nlm.nih.gov/pubmed/24813470)

Participation in research projects:

  • EXtention of academia-based PLATFORM to antidepressant hits discovery (PLATFORMex), Pol-Nor/198887/73/2013, function: executor, 2013 –
  • Innovative therapies for neurodegenerative and neurodevelopmental diseases based on mGlu receptor allosteric modulators – Allosterix, NCBiR 178469, function: executor, 2013 –
  • Antagonists of 5-HT6 receptor as advanced antipsychotic drugs with procognitive properties, UDA-POIG.01.03.01-12-063/09-02 (www.prokog.pl), function: executor, 2010-2013.

Scientific reports:

a) posters:

  1. Smusz, S.; Mordalski, S.; Witek, J.; Rataj, K.; Bojarski, A.J.; Automatic evaluation of complexes of ligands with serotonin receptors based on the application of machine learning methods; GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network, 07-09.10.2013, Warsaw, Poland, Poster
  2. Rataj, K.; Witek, J.; Kościółek, T.; Mordalski, S.; Bojarski, A.J.; Impact of template choice on homology model quality and their efficiency in Virtual Screening; GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network, 07-09.10.2013, Warsaw, Poland, Poster
  3. Witek, J.; Smusz, S.; Rataj, K.; Mordalski, S.; Bojarski, A.J.; An application of machine learning methods to Structural Interaction Fingerprints as a novel approach in the search for biologically active compounds; GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network, 07-09.10.2013, Warsaw, Poland, Poster
  4. Mordalski, S.; Witek, J.; Rataj, K.; Smusz, S.; Bojarski, A.J.; Automated docking restrains assignment based on interaction profiles; GPCR Workshop 2013, 01-05.12.2013, Maui, Hawaii, USA, Book of Abstracts, p.54. Poster
  5. Smusz, S.; Mordalski, S.; Witek, J.; Rataj, K.; Bojarski, A.J.; A novel machine learning-based protocol for predicting biological activity of chemical compounds; GPCR Workshop 2013, 01-05.12.2013, Maui, Hawaii, USA, Book of Abstracts, p.58. Poster
  6. Mordalski, S.; Witek, J.; Rataj, K.; Smusz, S.; Bojarski, A.J.; A SIFt-guided approach to docking restrains assignment. An application to Virtual Screening;  5th Symposium of the Polish Bioinformatics Society, 25-27.05.2012, Gdańsk, Poland, Book of Abstracts, p.Talk10. Abstract Poster
  7. Rataj, K.; Witek, J.; Kościółek, T.; Mordalski, S.; Bojarski, A.J.; Impact of template choice on quality of 5-HT6 receptor homology models; 5th Symposium of the Polish Bioinformatics Society, 25-27.05.2012, Gdańsk, Poland, Book of Abstracts, p.Poster33. Abstract Poster
  8. Witek, J.; Rataj, K.; Kościółek, T.; Mordalski, S.; Bojarski, A.J.; Structural Interaction Fingerprints as a tool for assessing ligand selectivity between two targets; 5th Symposium of the Polish Bioinformatics Society, 25-27.05.2012, Gdańsk, Poland, Book of Abstracts, p.Poster42. Abstract Poster
  9. Witek, J.; Rataj, K.; Mordalski, S.; Kościółek, T.; Bojarski, A.J.; Selected Transmembrane Receptors – Structures, Interactions and Binding Site Analysis; The 5th Conversatory of Medicinal Chemistry, 13-15.09.2012, Lublin, Poland, Book of Abstracts, p.P-87. Abstract Poster
  10. Rataj, K.; Witek, J.; Mordalski, S.; Kristiansen, K.; Smusz, S.; Bojarski, A.J.; Mutation Mining: Automated Extraction of Mutation Data from Scientific Publications; The 5th Conversatory of Medicinal Chemistry, 13-15.09.2012, Lublin, Poland, Book of Abstracts, p.P-59. Abstract Poster
  11. Witek, J.; Rataj, K.; Smusz, S.; Mordalski, S.; Kosciolek, T. Bojarski A.J. Application of Structural Interaction Fingerprints into post-docking analysis – insight into activity and selectivity, The 8. German Conference on Cheminformatics, 11-13.11.2012, Goslar, Niemcy, Book of Abstracts: P-30. Abstract Poster
  12. Rataj, K.; Witek, J.; Kosciolek, T.; Mordalski, S.; Bojarski A.J. The importance of template choice on homology modeling: A 5-HT6R-based study, The 8. German Conference on Cheminformatics, 11-13.11.2012, Goslar, Niemcy, Book of Abstracts: P-10 Abstract Poster
  13. Rataj, K.; Witek, J.; Kościółek, T.; Mordalski, S.; Bojarski, A.J.; Comparison of Homology Models of 5-HT6R Created with Different Crystal Templates; The 4th Conversatory of Medicinal Chemistry, 08-10.09.2011, Lublin, Poland, Book of Abstracts, p.P-52. Abstract Poster
  14. Witek, J.; Rataj, K.; Kościółek, T.; Mordalski, S.; Bojarski, A.J.; Application of Interaction Patterns to Discriminate Ligand Preference to Target/Antitarget Protein; The 4th Conversatory of Medicinal Chemistry, 08-10.09.2011, Lublin, Poland,  Book of Abstracts, p.P-73. Abstract Poster