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Items: 34


Building and rebuilding N-glycans in protein structure models.

van Beusekom B, Wezel N, Hekkelman ML, Perrakis A, Emsley P, Joosten RP.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):416-425. doi: 10.1107/S2059798319003875. Epub 2019 Apr 4.


A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop.

Roorda JC, Joosten RP, Perrakis A, Hiruma Y.

Proteins. 2019 Apr;87(4):348-352. doi: 10.1002/prot.25651. Epub 2019 Jan 8.


Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1.

van Beusekom B, Heidebrecht T, Adamopoulos A, Fish A, Pardon E, Steyaert J, Joosten RP, Perrakis A.

Acta Crystallogr F Struct Biol Commun. 2018 Nov 1;74(Pt 11):690-695. doi: 10.1107/S2053230X18010282. Epub 2018 Oct 16.


Homology-based loop modeling yields more complete crystallographic protein structures.

van Beusekom B, Joosten K, Hekkelman ML, Joosten RP, Perrakis A.

IUCrJ. 2018 Aug 8;5(Pt 5):585-594. doi: 10.1107/S2052252518010552. eCollection 2018 Sep 1.


Making glycoproteins a little bit sweeter with PDB-REDO.

van Beusekom B, Lütteke T, Joosten RP.

Acta Crystallogr F Struct Biol Commun. 2018 Aug 1;74(Pt 8):463-472. doi: 10.1107/S2053230X18004016. Epub 2018 Jul 26.


An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein.

Delbart F, Brams M, Gruss F, Noppen S, Peigneur S, Boland S, Chaltin P, Brandao-Neto J, von Delft F, Touw WG, Joosten RP, Liekens S, Tytgat J, Ulens C.

J Biol Chem. 2018 Feb 16;293(7):2534-2545. doi: 10.1074/jbc.M117.815316. Epub 2017 Dec 13.


Homology-based hydrogen bond information improves crystallographic structures in the PDB.

van Beusekom B, Touw WG, Tatineni M, Somani S, Rajagopal G, Luo J, Gilliland GL, Perrakis A, Joosten RP.

Protein Sci. 2018 Mar;27(3):798-808. doi: 10.1002/pro.3353. Epub 2017 Dec 8.


Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures.

Hiruma Y, Koch A, Hazraty N, Tsakou F, Medema RH, Joosten RP, Perrakis A.

J Biol Chem. 2017 Sep 1;292(35):14496-14504. doi: 10.1074/jbc.M117.783555. Epub 2017 Jul 18.


Carbohydrate 3D structure validation.

Joosten RP, Lütteke T.

Curr Opin Struct Biol. 2017 Jun;44:9-17. doi: 10.1016/ Epub 2016 Nov 4. Review.


Validation and correction of Zn-CysxHisy complexes.

Touw WG, van Beusekom B, Evers JM, Vriend G, Joosten RP.

Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1110-1118. Epub 2016 Sep 15.


Structural basis of reversine selectivity in inhibiting Mps1 more potently than aurora B kinase.

Hiruma Y, Koch A, Dharadhar S, Joosten RP, Perrakis A.

Proteins. 2016 Dec;84(12):1761-1766. doi: 10.1002/prot.25174. Epub 2016 Oct 11.


Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin.

Hausmann J, Keune WJ, Hipgrave Ederveen AL, van Zeijl L, Joosten RP, Perrakis A.

J Struct Biol. 2016 Aug;195(2):199-206. doi: 10.1016/j.jsb.2016.06.002. Epub 2016 Jun 4.


Data Mining of Macromolecular Structures.

van Beusekom B, Perrakis A, Joosten RP.

Methods Mol Biol. 2016;1415:107-38. doi: 10.1007/978-1-4939-3572-7_6.


Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.

Keune WJ, Hausmann J, Bolier R, Tolenaars D, Kremer A, Heidebrecht T, Joosten RP, Sunkara M, Morris AJ, Matas-Rico E, Moolenaar WH, Oude Elferink RP, Perrakis A.

Nat Commun. 2016 Apr 14;7:11248. doi: 10.1038/ncomms11248.


The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex.

Dym O, Song W, Felder C, Roth E, Shnyrov V, Ashani Y, Xu Y, Joosten RP, Weiner L, Sussman JL, Silman I.

Protein Sci. 2016 Jun;25(6):1096-114. doi: 10.1002/pro.2923. Epub 2016 Mar 28.


New Biological Insights from Better Structure Models.

Touw WG, Joosten RP, Vriend G.

J Mol Biol. 2016 Mar 27;428(6):1375-1393. doi: 10.1016/j.jmb.2016.02.002. Epub 2016 Feb 8. Review.


Detection of trans-cis flips and peptide-plane flips in protein structures.

Touw WG, Joosten RP, Vriend G.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi: 10.1107/S1399004715008263. Epub 2015 Jul 28.


The first step of peptide selection in antigen presentation by MHC class I molecules.

Garstka MA, Fish A, Celie PH, Joosten RP, Janssen GM, Berlin I, Hoppes R, Stadnik M, Janssen L, Ovaa H, van Veelen PA, Perrakis A, Neefjes J.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1505-10. doi: 10.1073/pnas.1416543112. Epub 2015 Jan 20.


A series of PDB-related databanks for everyday needs.

Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.

Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8. doi: 10.1093/nar/gku1028. Epub 2014 Oct 28.


The PDB_REDO server for macromolecular structure model optimization.

Joosten RP, Long F, Murshudov GN, Perrakis A.

IUCrJ. 2014 May 30;1(Pt 4):213-20. doi: 10.1107/S2052252514009324. eCollection 2014 Jul 1.


High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies.

Rimsa V, Eadsforth TC, Joosten RP, Hunter WN.

Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):279-89. doi: 10.1107/S1399004713026801. Epub 2014 Jan 29.


Timely deposition of macromolecular structures is necessary for peer review.

Joosten RP, Soueidan H, Wessels LF, Perrakis A.

Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2293-5. doi: 10.1107/S0907444913024621. Epub 2013 Nov 19.


The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.

Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G.

J Cheminform. 2013 Jul 29;5(1):36. doi: 10.1186/1758-2946-5-36.


Structure of NPP1, an ectonucleotide pyrophosphatase/phosphodiesterase involved in tissue calcification.

Jansen S, Perrakis A, Ulens C, Winkler C, Andries M, Joosten RP, Van Acker M, Luyten FP, Moolenaar WH, Bollen M.

Structure. 2012 Nov 7;20(11):1948-59. doi: 10.1016/j.str.2012.09.001. Epub 2012 Oct 4.


PDB_REDO: constructive validation, more than just looking for errors.

Joosten RP, Joosten K, Murshudov GN, Perrakis A.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):484-96. doi: 10.1107/S0907444911054515. Epub 2012 Mar 16.


Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A.

Bioinformatics. 2011 Dec 15;27(24):3392-8. doi: 10.1093/bioinformatics/btr590. Epub 2011 Oct 27.


A new generation of crystallographic validation tools for the protein data bank.

Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.

Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006.


The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1.

Heidebrecht T, Christodoulou E, Chalmers MJ, Jan S, Ter Riet B, Grover RK, Joosten RP, Littler D, van Luenen H, Griffin PR, Wentworth P Jr, Borst P, Perrakis A.

Nucleic Acids Res. 2011 Jul;39(13):5715-28. doi: 10.1093/nar/gkr125. Epub 2011 Mar 16.


A series of PDB related databases for everyday needs.

Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G.

Nucleic Acids Res. 2011 Jan;39(Database issue):D411-9. doi: 10.1093/nar/gkq1105. Epub 2010 Nov 11.


Homology modelling and spectroscopy, a never-ending love story.

Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G.

Eur Biophys J. 2010 Mar;39(4):551-63. doi: 10.1007/s00249-009-0531-0. Epub 2009 Aug 29. Review.


PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G.

J Appl Crystallogr. 2009 Jun 1;42(Pt 3):376-384. Epub 2009 Apr 3.


Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

Joosten RP, Womack T, Vriend G, Bricogne G.

Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):176-85. doi: 10.1107/S0907444908037591. Epub 2009 Jan 20.


PDB improvement starts with data deposition.

Joosten RP, Vriend G.

Science. 2007 Jul 13;317(5835):195-6. No abstract available.


Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding.

Smith BJ, Huyton T, Joosten RP, McKimm-Breschkin JL, Zhang JG, Luo CS, Lou MZ, Labrou NE, Garrett TP.

Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):947-52. Epub 2006 Aug 19.


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