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CING: an integrated residue-based structure validation program suite

Jurgen F. Doreleijers, Alan W. Sousa da Silva, Elmar Krieger, Sander B. Nabuurs, Christian A. E. M. Spronk, Tim J. Stevens, Wim F. Vranken, Gert Vriend, Geerten W. Vuister
<span title="2012-09-18">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
Surveys by ourselves (Doreleijers et al. 1998; Hooft et al. 1996b; Nabuurs et al. 2005 Nabuurs et al. , 2006 , and others e.g.  ...  r154 Doreleijers et al. (2005) nmr.cmbi.ru.nl/*jd/wattos WHAT_CHECK ? 2010-08-16 Hooft et al. (1996b) swift.cmbi.ru.nl/gv/whatcheck Xplor-NIH ?  ... 
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The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Jurgen F. Doreleijers, Wim F. Vranken, Christopher Schulte, Jundong Lin, Jonathan R. Wedell, Christopher J. Penkett, Geerten W. Vuister, Gert Vriend, John L. Markley, Eldon L. Ulrich
<span title="2009-10-07">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
(f) Last but not least, the NRG data should be integrated with the main BMRB data on chemical shifts that will soon be mandatory for PDB submission.  ...  The initial version of the NRG included data from only 97 PDB entries (a database named ''DB97'') (Doreleijers et al. 1998 ); in 2003 we had 545 entries (Doreleijers et al. 2003 ) and the previous version  ... 
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The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc

Astrid P.A.M. Eijkelenboom, Fusinita M.I. van den Ent, Arnold Vos, Jurgen F. Doreleijers, Karl Hård, Thomas D. Tullius, Ronald H.A. Plasterk, Robert Kaptein, Rolf Boelens
<span title="">1997</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/waxwzq3cnbet3cmwccpuk4bel4" style="color: black;">Current Biology</a> </i> &nbsp;
Bond angles were restrained to 126°f or Zn-HisN ε2 -HisC ε1 /C δ2 and Zn-HisN δ1 -C ε1 /C γ and to 100° for Zn-CysS γ -CysC β .  ... 
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CASD-NMR: critical assessment of automated structure determination by NMR

Antonio Rosato, Anurag Bagaria, David Baker, Benjamin Bardiaux, Andrea Cavalli, Jurgen F Doreleijers, Andrea Giachetti, Paul Guerry, Peter Güntert, Torsten Herrmann, Yuanpeng J Huang, Hendrik R A Jonker (+9 others)
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth0909-625">doi:10.1038/nmeth0909-625</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19718014">pmid:19718014</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2841015/">pmcid:PMC2841015</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bm3h47ql4rhfrp633cj7ntrkvy">fatcat:bm3h47ql4rhfrp633cj7ntrkvy</a> </span>
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RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank

Aart J. Nederveen, Jurgen F. Doreleijers, Wim Vranken, Zachary Miller, Chris A.E.M. Spronk, Sander B. Nabuurs, Peter Güntert, Miron Livny, John L. Markley, Michael Nilges, Eldon L. Ulrich, Robert Kaptein (+1 others)
<span title="2005-04-08">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
f RMSD relative to average coordinates of original ensemble from ORG set. TABLE II .  ...  Precision NMR ensemble e Backbone RMSD (Å) 2.3 Ϯ 2.8 2.9 Ϯ 3.2 2.8 Ϯ 3.7 2.9 Ϯ 3.1 2.8 Ϯ 3.6 Well-ordered RMSD (Å) 0.6 Ϯ 1.0 1.0 Ϯ 1.4 1.0 Ϯ 1.4 1.1 Ϯ 1.4 1.0 Ϯ 1.4 Backbone RMSD ORG (Å) f  ... 
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Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Antonio Rosato, James M. Aramini, Cheryl Arrowsmith, Anurag Bagaria, David Baker, Andrea Cavalli, Jurgen F. Doreleijers, Alexander Eletsky, Andrea Giachetti, Paul Guerry, Aleksandras Gutmanas, Peter Güntert (+25 others)
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
., 2009) for the backbone torsion angles f and c of non-proline residues, with a prediction classified as ''good'' by TALOS+.  ...  Dihedral angle restraints were generated from chemical shifts with the program TALOS+ (Shen et al., 2009) for the backbone torsion angles f and c.  ... 
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WeNMR: Structural Biology on the Grid

Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini (+24 others)
<span title="2012-11-30">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qrfhtnmiezbrbd2wgd2gragrxi" style="color: black;">Journal of Grid Computing</a> </i> &nbsp;
T.A. Wassenaar et al. molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used
more &raquo; ... in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI).
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A global analysis of NMR distance constraints from the PDB

Wim Vranken
<span title="2007-10-09">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
Acknowledgements The author thanks Aart Nederveen and Jurgen Doreleijers for the RECOORD and DOCR/FRED collaborations that were instrumental in creating the setup to harmonise constraints and coordinates  ...  The original 409 mappings from the RECOORD project (by Aart Nederveen) and a further mappings 124 by the author and 17 by Jurgen Doreleijers were used to correctly set the PDB-constraint file mapping for  ...  a m r o f n I ) L M T H ( o f n i d e t a l l o C ) y r a n o i t c i d n o h t y P ( e t a d i l a V r e t l i F (2) Protein secondary structure analysis: Groups interatomic distances by secondary structure  ... 
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Elsewhere in biology

<span title="">1997</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/v6fzdolajra2detrgb2pojrdpm" style="color: black;">Chemistry and Biology</a> </i> &nbsp;
Astrid PAM Eijkelenboom, Fusinita MI van den Ent, Arnold Vos, Jurgen F Doreleijers, Karl Hard, Thomas D Tullius, Ronald HA Plasterk, Robert Kaptein and Rolf Boelens (1997).  ...  Three domains have been identified in HIV integrase: an amino-terminal domain, a central catalytic core and a carboxy-terminal Antonio Casamayor, F Barry Caudwell, Nick Morrice, David G Norman,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1074-5521(97)90121-6">doi:10.1016/s1074-5521(97)90121-6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4sg3jsd4d5hk3ctxth5vp4y5a4">fatcat:4sg3jsd4d5hk3ctxth5vp4y5a4</a> </span>
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Paper Alert

Robert Liddington, Christin Frederick
<span title="">1998</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
Jurgen F Doreleijers, Johan AC Rullmann, Robert Kaptein (1998) . J. Mol. Biol. 281, [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0969-2126(98)00133-6">doi:10.1016/s0969-2126(98)00133-6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dh3ycj3gtzaspcmkdug5jngjdq">fatcat:dh3ycj3gtzaspcmkdug5jngjdq</a> </span>
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Concepts and tools for NMR restraint analysis and validation

Sander B. Nabuurs, Chris A.E.M. Spronk, Gert Vriend, Geerten W. Vuister
<span title="">2004</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mer6etey4vcqlknlhgfusgt4ze" style="color: black;">Concepts in magnetic resonance</a> </i> &nbsp;
[2] . d F1,F2 ϭ ͩ kϭ1 N͑F1,F2͒ d k Ϫ6 ͪ Ϫ1/6 [2] where k runs through all N(F 1 , F 2 ) contributions to a crosspeak at frequencies F 1 and F 2 , and d k is the distance between the two protons corresponding  ...  Finally, the AQUA program suite can be downloaded from http://urchin.bmrb.wisc.edu/ϳjurgen/aqua/. Figure 1 ( 1 A) Ensemble of 30 structural models of GB1 (8 ).  ... 
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Prävention Von Jugendgewalt: Eine Auseinandersetzung Mit Der Forderung Nach Geschlechtsspezifischer Prävention

Larisa Nussbaum, Daniel Kilchmann
<span title="2011-08-15">2011</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Raithel & Jürgen Mansel, 2003, S. 25; Theo Doreleijers, Matthias Jäger & Daniel Gutschner, 2008, S. 29).  ...  (Seifert-Wieczorkowsky, 2009, S. 207 f.)  ... 
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Psychisch erkrankte Jugendliche im Massnahmenvollzug: Sozialpädagogische Arbeit im Wohnalltag unter Berücksichtigung der psychischen Störung mit dem Ziel einer förderlichen Entwicklung Diese

Deborah Schwarzentruber, Fabienne Fischer
<span title="2019-08-15">2019</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Dieter F.  ...  (Dieter F.  ... 
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