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New ways to boost molecular dynamics simulations.
Krieger E, Vriend G. Krieger E, et al. Among authors: vriend g. 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. Among authors: vriend g. 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. Among authors: vriend g. Methods Biochem Anal. 2003;44:509-23. doi: 10.1002/0471721204.ch25. Methods Biochem Anal. 2003. PMID: 12647402 Review. No abstract available.
Molecular determinants of the interaction of Mad with the PAH2 domain of mSin3.
Le Guezennec X, Vriend G, Stunnenberg HG. Le Guezennec X, et al. Among authors: vriend g. J Biol Chem. 2004 Jun 11;279(24):25823-9. doi: 10.1074/jbc.M313860200. Epub 2004 Mar 26. J Biol Chem. 2004. PMID: 15047710
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. Among authors: vriend g. Proteins. 2004 Dec 1;57(4):678-83. doi: 10.1002/prot.20251. Proteins. 2004. PMID: 15390263
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.
Nabuurs SB, Spronk CA, Vuister GW, Vriend G. Nabuurs SB, et al. Among authors: vriend g. PLoS Comput Biol. 2006 Feb;2(2):e9. doi: 10.1371/journal.pcbi.0020009. Epub 2006 Feb 3. PLoS Comput Biol. 2006. PMID: 16462939 Free PMC article.
Fast empirical pKa prediction by Ewald summation.
Krieger E, Nielsen JE, Spronk CA, Vriend G. Krieger E, et al. Among authors: vriend g. 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
Negative constraints underlie the ErbB specificity of epidermal growth factor-like ligands.
van der Woning SP, van Rotterdam W, Nabuurs SB, Venselaar H, Jacobs-Oomen S, Wingens M, Vriend G, Stortelers C, van Zoelen EJ. van der Woning SP, et al. Among authors: vriend g. J Biol Chem. 2006 Dec 29;281(52):40033-40. doi: 10.1074/jbc.M603168200. Epub 2006 Oct 10. J Biol Chem. 2006. PMID: 17032651
Stabilization of peptide fibrils by hydrophobic interaction.
Meijer JT, Roeters M, Viola V, Löwik DW, Vriend G, van Hest JC. Meijer JT, et al. Among authors: vriend g. Langmuir. 2007 Feb 13;23(4):2058-63. doi: 10.1021/la0625345. Langmuir. 2007. PMID: 17279695
Correlated mutation analyses on super-family alignments reveal functionally important residues.
Kuipers RK, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NG, van Berkel WJ, Vriend G, Schaap PJ. Kuipers RK, et al. Among authors: vriend g. Proteins. 2009 Aug 15;76(3):608-16. doi: 10.1002/prot.22374. Proteins. 2009. PMID: 19274741
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