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New ways to boost molecular dynamics simulations.
Krieger E, Vriend G. Krieger E, et al. J Comput Chem. 2015 May 15;36(13):996-1007. doi: 10.1002/jcc.23899. Epub 2015 Mar 30. J Comput Chem. 2015. PMID: 25824339 Free PMC article.
Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.
Krieger E, Koraimann G, Vriend G. Krieger E, et al. Proteins. 2002 May 15;47(3):393-402. doi: 10.1002/prot.10104. Proteins. 2002. PMID: 11948792
Homology modeling.
Krieger E, Nabuurs SB, Vriend G. Krieger E, et al. Methods Biochem Anal. 2003;44:509-23. doi: 10.1002/0471721204.ch25. Methods Biochem Anal. 2003. PMID: 12647402 Review. No abstract available.
A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase.
Koenderink JB, Swarts HG, Willems PH, Krieger E, De Pont JJ. Koenderink JB, et al. Among authors: krieger e. J Biol Chem. 2004 Apr 16;279(16):16417-24. doi: 10.1074/jbc.M400020200. Epub 2004 Feb 3. J Biol Chem. 2004. PMID: 14761952
A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.
Krieger E, Geretti E, Brandner B, Goger B, Wells TN, Kungl AJ. Krieger E, et al. Proteins. 2004 Mar 1;54(4):768-75. doi: 10.1002/prot.10590. Proteins. 2004. PMID: 14997572
Identification and molecular modelling of a mutation in the motor head domain of myosin VIIA in a family with autosomal dominant hearing impairment (DFNA11).
Luijendijk MW, Van Wijk E, Bischoff AM, Krieger E, Huygen PL, Pennings RJ, Brunner HG, Cremers CW, Cremers FP, Kremer H. Luijendijk MW, et al. Among authors: krieger e. Hum Genet. 2004 Jul;115(2):149-56. doi: 10.1007/s00439-004-1137-3. Epub 2004 Jun 2. Hum Genet. 2004. PMID: 15221449
Making optimal use of empirical energy functions: force-field parameterization in crystal space.
Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. Krieger E, et al. Proteins. 2004 Dec 1;57(4):678-83. doi: 10.1002/prot.20251. Proteins. 2004. PMID: 15390263
Asn792 participates in the hydrogen bond network around the K+-binding pocket of gastric H,K-ATPase.
Swarts HG, Koenderink JB, Willems PH, Krieger E, De Pont JJ. Swarts HG, et al. Among authors: krieger e. J Biol Chem. 2005 Mar 25;280(12):11488-94. doi: 10.1074/jbc.M412321200. Epub 2005 Jan 11. J Biol Chem. 2005. PMID: 15644331
A direct role in K+ binding was postulated for Na,K-ATPase but was not found in a recent model for gastric H,K-ATPase (Koenderink, J. B., Swarts, H. G. P., Willems, P. H. G. M., Krieger, E., and De Pont, J. J. H. H. M. (2004) J. Biol. Chem. 279, 16417-16424). ...
A direct role in K+ binding was postulated for Na,K-ATPase but was not found in a recent model for gastric H,K-ATPase (Koenderink, J. B., Sw …
Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acids.
Qiu LY, Krieger E, Schaftenaar G, Swarts HG, Willems PH, De Pont JJ, Koenderink JB. Qiu LY, et al. Among authors: krieger e. J Biol Chem. 2005 Sep 16;280(37):32349-55. doi: 10.1074/jbc.M505168200. Epub 2005 Jul 28. J Biol Chem. 2005. PMID: 16051601
Fast empirical pKa prediction by Ewald summation.
Krieger E, Nielsen JE, Spronk CA, Vriend G. Krieger E, et al. J Mol Graph Model. 2006 Dec;25(4):481-6. doi: 10.1016/j.jmgm.2006.02.009. Epub 2006 Apr 27. J Mol Graph Model. 2006. PMID: 16644253
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