Elmar Krieger

Summary

Publications

  1. ncbi request reprint Making optimal use of empirical energy functions: force-field parameterization in crystal space
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    Proteins 57:678-83. 2004
  2. ncbi request reprint Definition of a new information-based per-residue quality parameter
    Sander B Nabuurs
    Center for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen, Toernooiveld 1, 6525, ED, Nijmegen, The Netherlands
    J Biomol NMR 33:123-34. 2005
  3. ncbi request reprint Quantitative evaluation of experimental NMR restraints
    Sander B Nabuurs
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands
    J Am Chem Soc 125:12026-34. 2003
  4. ncbi request reprint Fast empirical pKa prediction by Ewald summation
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, The Netherlands
    J Mol Graph Model 25:481-6. 2006
  5. doi request reprint Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Methods Mol Biol 819:405-21. 2012
  6. ncbi request reprint Homology modeling
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    Methods Biochem Anal 44:509-23. 2003
  7. ncbi request reprint The precision of NMR structure ensembles revisited
    Chris A E M Spronk
    Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands
    J Biomol NMR 25:225-34. 2003
  8. ncbi request reprint MPP1 links the Usher protein network and the Crumbs protein complex in the retina
    Ilse Gosens
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Hum Mol Genet 16:1993-2003. 2007
  9. ncbi request reprint A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations
    Elmar Krieger
    Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    Proteins 54:768-75. 2004
  10. pmc Interaction of nephrocystin-4 and RPGRIP1 is disrupted by nephronophthisis or Leber congenital amaurosis-associated mutations
    Ronald Roepman
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, P O Box 9101, 6500 HB, Nijmegen, The Netherlands
    Proc Natl Acad Sci U S A 102:18520-5. 2005

Collaborators

Detail Information

Publications20

  1. ncbi request reprint Making optimal use of empirical energy functions: force-field parameterization in crystal space
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    Proteins 57:678-83. 2004
    ..Due to its compatibility with the well-established AMBER format, YAMBER can be used by almost any molecular dynamics program. The parameters are freely available from www.yasara.org/yamber...
  2. ncbi request reprint Definition of a new information-based per-residue quality parameter
    Sander B Nabuurs
    Center for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen, Toernooiveld 1, 6525, ED, Nijmegen, The Netherlands
    J Biomol NMR 33:123-34. 2005
    ..From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data...
  3. ncbi request reprint Quantitative evaluation of experimental NMR restraints
    Sander B Nabuurs
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands
    J Am Chem Soc 125:12026-34. 2003
    ..Because our method describes the quantitative evaluation of experimental NMR restraints, we propose the acronym QUEEN...
  4. ncbi request reprint Fast empirical pKa prediction by Ewald summation
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, The Netherlands
    J Mol Graph Model 25:481-6. 2006
    ..A reliable null-model to judge pK(a) prediction accuracies is also presented...
  5. doi request reprint Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Methods Mol Biol 819:405-21. 2012
    ..An implementation of the algorithm has been available since 2008 as part of the YASARA modeling & simulation program...
  6. ncbi request reprint Homology modeling
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    Methods Biochem Anal 44:509-23. 2003
  7. ncbi request reprint The precision of NMR structure ensembles revisited
    Chris A E M Spronk
    Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands
    J Biomol NMR 25:225-34. 2003
    ..This maximized RMSD therefore seems a better estimate of the true uncertainty in the atomic coordinates...
  8. ncbi request reprint MPP1 links the Usher protein network and the Crumbs protein complex in the retina
    Ilse Gosens
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Hum Mol Genet 16:1993-2003. 2007
    ..These processes, essential in neural development and patterning of the retina, may be disrupted in eye disorders that are associated with defects in these protein networks...
  9. ncbi request reprint A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations
    Elmar Krieger
    Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    Proteins 54:768-75. 2004
    ..Isothermal fluorescence titration experiments using differently sulfated heparin disaccharides confirmed that a single disaccharide can indeed bind IL-8 with high affinity...
  10. pmc Interaction of nephrocystin-4 and RPGRIP1 is disrupted by nephronophthisis or Leber congenital amaurosis-associated mutations
    Ronald Roepman
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, P O Box 9101, 6500 HB, Nijmegen, The Netherlands
    Proc Natl Acad Sci U S A 102:18520-5. 2005
    ..Thus, we provide evidence for the involvement of this disrupted interaction in the retinal dystrophy of both SLSN and LCA patients...
  11. pmc CING: an integrated residue-based structure validation program suite
    Jurgen F Doreleijers
    CMBI, Radboud University Medical Centre, Geert Grooteplein 26 28, 6525 GA Nijmegen, The Netherlands
    J Biomol NMR 54:267-83. 2012
    ..The publically accessible, secure iCing webserver ( https://nmr.le.ac.uk ) allows individual users to upload the NMR data and run a CING validation analysis...
  12. ncbi request reprint Models@Home: distributed computing in bioinformatics using a screensaver based approach
    Elmar Krieger
    CMBI, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    Bioinformatics 18:315-8. 2002
    ..berkeley.edu), the world's largest distributed computing project...
  13. ncbi request reprint Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field
    Elmar Krieger
    Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
    Proteins 47:393-402. 2002
    ..A new method to assign force-field parameters based on molecular trees is also presented. A NOVA server is freely accessible at http://www.yasara.com/servers..
  14. ncbi request reprint A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase
    Jan B Koenderink
    Department of Biochemistry, Nijmegen Center for Molecular Life Sciences, University of Nijmegen, Nijmegen, The Netherlands
    J Biol Chem 279:16417-24. 2004
    ..Moreover, its breakage (E820Q) can generate a K+-insensitive activity and an E1 preference. In addition, the study gives a molecular explanation for the electroneutrality of H,K-ATPases...
  15. ncbi request reprint MYO15A (DFNB3) mutations in Turkish hearing loss families and functional modeling of a novel motor domain mutation
    Ersan Kalay
    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Am J Med Genet A 143:2382-9. 2007
    ....
  16. ncbi request reprint Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acids
    Li Yan Qiu
    Department of Biochemistry 160, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, The Netherlands
    J Biol Chem 280:32349-55. 2005
    ..Based on the E(2)P crystal structure of Ca(2+)-ATPase we constructed a homology model for the ouabain-binding site of Na,K-ATPase involving all seven amino acids as well as several earlier postulated amino acids...
  17. ncbi request reprint Asn792 participates in the hydrogen bond network around the K+-binding pocket of gastric H,K-ATPase
    Herman G P Swarts
    Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, P O Box 9101, 6500 HB Nijmegen, The Netherlands
    J Biol Chem 280:11488-94. 2005
    ..These data strongly support the validity of the model in which Asn792 participates in the hydrogen bond network around the K(+)-binding pocket...
  18. ncbi request reprint GTP-Ras disrupts the intramolecular complex of C1 and RA domains of Nore1
    Elena Harjes
    Molecular and Structural Biophysics, Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, D 44227 Dortmund, Germany
    Structure 14:881-8. 2006
    ..Once the C1 domain tumbles freely in solution, a lipid binding interface becomes accessible. Furthermore, we provide evidence of phosphatidylinositol 3-phosphate binding of the free C1 domain...
  19. doi request reprint Functional role of arginine 375 in transmembrane helix 6 of multidrug resistance protein 4 (MRP4/ABCC4)
    Azza A K El-Sheikh
    Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, P O Box 9101, 6500 HB Nijmegen, The Netherlands
    Mol Pharmacol 74:964-71. 2008
    ..A homology model of MRP4 showed that Arg375 and Arg998 face right into the central aqueous pore of MRP4. We conclude that positively charged amino acids in transmembrane helices 6 and 12 contribute to the MRP4 substrate-binding pocket...
  20. ncbi request reprint Gain-of-function mutation in ADULT syndrome reveals the presence of a second transactivation domain in p63
    Pascal H G Duijf
    Department of Human Genetics 417, University Medical Centre Nijmegen, Box 9101, 6500 HB Nijmegen, The Netherlands
    Hum Mol Genet 11:799-804. 2002
    ..Our results further show that p63 contains a second transactivation domain which is normally repressed and can become activated by mutations in the DNA binding domain of p63...