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New restraints and validation approaches for nucleic acid structures in PDB-REDO.
de Vries I, Kwakman T, Lu XJ, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP. de Vries I, et al. Among authors: perrakis a. Acta Crystallogr D Struct Biol. 2021 Sep 1;77(Pt 9):1127-1141. doi: 10.1107/S2059798321007610. Epub 2021 Aug 24. Acta Crystallogr D Struct Biol. 2021. PMID: 34473084 Free PMC article.
Towards complete validated models in the next generation of ARP/wARP.
Cohen SX, Morris RJ, Fernandez FJ, Ben Jelloul M, Kakaris M, Parthasarathy V, Lamzin VS, Kleywegt GJ, Perrakis A. Cohen SX, et al. Among authors: perrakis a. Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2222-9. doi: 10.1107/S0907444904027556. Epub 2004 Nov 26. Acta Crystallogr D Biol Crystallogr. 2004. PMID: 15572775
A knowledge-driven approach for crystallographic protein model completion.
Joosten K, Cohen SX, Emsley P, Mooij W, Lamzin VS, Perrakis A. Joosten K, et al. Among authors: perrakis a. Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):416-24. doi: 10.1107/S0907444908001558. Epub 2008 Mar 19. Acta Crystallogr D Biol Crystallogr. 2008. PMID: 18391408 Free PMC article.
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. Read RJ, et al. Among authors: perrakis a. Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006. Structure. 2011. PMID: 22000512 Free PMC article.
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.
Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A. Joosten RP, et al. Among authors: perrakis a. Bioinformatics. 2011 Dec 15;27(24):3392-8. doi: 10.1093/bioinformatics/btr590. Epub 2011 Oct 27. Bioinformatics. 2011. PMID: 22034521 Free PMC article.
MOTIVATION: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. ...CONTACT: r.joosten@nki.nl; a.per …
MOTIVATION: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological p …
PDB_REDO: constructive validation, more than just looking for errors.
Joosten RP, Joosten K, Murshudov GN, Perrakis A. Joosten RP, et al. Among authors: perrakis a. Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):484-96. doi: 10.1107/S0907444911054515. Epub 2012 Mar 16. Acta Crystallogr D Biol Crystallogr. 2012. PMID: 22505269 Free PMC article.
242 results