Research Topics
Genomes and Genes | Elmar KriegerSummaryAffiliation: Radboud University Nijmegen Country: The Netherlands Publications
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Publications
Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimizationElmar 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...
Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acidsLi 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...- Phenylalanine 368 of multidrug resistance-associated protein 4 (MRP4/ABCC4) plays a crucial role in substrate-specific transport activityHanneke G M Wittgen
Department of Pharmacology and Toxicology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, The Netherlands
Biochem Pharmacol 84:366-73. 2012..They, however, might interact with the substrates during rearrangement of helixes for substrate translocation, funneling the substrates to the exit site in the outward-facing conformation... - Fast empirical pKa prediction by Ewald summationElmar 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... - Definition of a new information-based per-residue quality parameterSander 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... - 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... 
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8Elmar Krieger
Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, The Netherlands
Proteins 77:114-22. 2009....- Making optimal use of empirical energy functions: force-field parameterization in crystal spaceElmar 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... - A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrationsElmar 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... - Quantitative evaluation of experimental NMR restraintsSander 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... - Homology modelingElmar Krieger
Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
Methods Biochem Anal 44:509-23. 2003 - MPP1 links the Usher protein network and the Crumbs protein complex in the retinaIlse 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... - Interaction of nephrocystin-4 and RPGRIP1 is disrupted by nephronophthisis or Leber congenital amaurosis-associated mutationsRonald 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... - CING: an integrated residue-based structure validation program suiteJurgen 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... - Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force fieldElmar 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.. - Models@Home: distributed computing in bioinformatics using a screensaver based approachElmar Krieger
CMBI, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
Bioinformatics 18:315-8. 2002..We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance... - MYO15A (DFNB3) mutations in Turkish hearing loss families and functional modeling of a novel motor domain mutationErsan Kalay
Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
Am J Med Genet A 143:2382-9. 2007.... - A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPaseJan 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...