TY - JOUR AU - Anfinsen, C. B. PY - 1973 DA - 1973// TI - Principles that govern the folding of protein chains JO - Science (New York, NY) VL - 181 UR - https://doi.org/10.1126/science.181.4096.223 DO - 10.1126/science.181.4096.223 ID - Anfinsen1973 ER - TY - JOUR AU - Bradley, P. AU - Misura, K. M. S. AU - Baker, D. PY - 2005 DA - 2005// TI - Toward high-resolution de novo structure prediction for small proteins JO - Science (New York, NY) VL - 309 UR - https://doi.org/10.1126/science.1113801 DO - 10.1126/science.1113801 ID - Bradley2005 ER - TY - CHAP AU - Rhodes, G. AU - Cooper, J. PY - 2006 DA - 2006// TI - Model and molecule BT - Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models UR - https://doi.org/10.1016/B978-012587073-3/50003-9 DO - 10.1016/B978-012587073-3/50003-9 ID - Rhodes2006 ER - TY - JOUR AU - Berman, H. AU - Henrick, K. AU - Nakamura, H. PY - 2003 DA - 2003// TI - Announcing the worldwide protein data bank JO - Nat Struct Biol VL - 10 UR - https://doi.org/10.1038/nsb1203-980 DO - 10.1038/nsb1203-980 ID - Berman2003 ER - TY - JOUR AU - Dauter, Z. AU - Weiss, M. S. AU - Einspahr, H. AU - Baker, E. N. PY - 2013 DA - 2013// TI - Expectation bias and information content JO - Acta Crystallogr Sect D Struct Biol Cryst VL - 69 UR - https://doi.org/10.1107/S0907444913000255 DO - 10.1107/S0907444913000255 ID - Dauter2013 ER - TY - JOUR AU - Bränd’en, C. -. I. AU - Alwyn Jones, T. PY - 1990 DA - 1990// TI - Between objectivity and subjectivity JO - Nature VL - 343 UR - https://doi.org/10.1038/343687a0 DO - 10.1038/343687a0 ID - Bränd’en1990 ER - TY - JOUR AU - Jones, T. A. AU - Zou, J. Y. AU - Cowan, S. W. AU - Kjeldgaard, M. PY - 1991 DA - 1991// TI - Improved methods for building protein models in electron density maps and the location of errors in these models JO - Acta Crystallogr Sect A Found Cryst VL - 47 UR - https://doi.org/10.1107/S0108767390010224 DO - 10.1107/S0108767390010224 ID - Jones1991 ER - TY - JOUR AU - Read, R. J. AU - Adams, P. D. AU - Arendall, W. B. AU - Brunger, A. T. AU - Emsley, P. AU - Joosten, R. P. AU - Kleywegt, G. J. AU - Krissinel, E. B. AU - Lütteke, T. AU - Otwinowski, Z. AU - Perrakis, A. AU - Richardson, J. S. AU - Sheffler, W. H. AU - Smith, J. L. AU - Tickle, I. J. AU - Vriend, G. AU - Zwart, P. H. PY - 2011 DA - 2011// TI - A new generation of crystallographic validation tools for the protein data bank JO - Structure (London, England: 1993) VL - 19 UR - https://doi.org/10.1016/j.str.2011.08.006 DO - 10.1016/j.str.2011.08.006 ID - Read2011 ER - TY - JOUR AU - Gore, S. AU - Velankar, S. AU - Kleywegt, G. J. PY - 2012 DA - 2012// TI - Implementing an x-ray validation pipeline for the protein data bank JO - Acta Crystallogr Sect D Biol Cryst VL - 68 UR - https://doi.org/10.1107/S0907444911050359 DO - 10.1107/S0907444911050359 ID - Gore2012 ER - TY - JOUR AU - Richardson, J. S. AU - Richardson, D. C. PY - 2013 DA - 2013// TI - Studying and polishing the PDB’s macromolecules JO - Biopolymers VL - 99 UR - https://doi.org/10.1002/bip.22108 DO - 10.1002/bip.22108 ID - Richardson2013 ER - TY - JOUR AU - Pozharski, E. AU - Weichenberger, C. X. AU - Rupp, B. PY - 2013 DA - 2013// TI - Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures JO - Acta Crystallogr Sect D Biol Cryst VL - 69 UR - https://doi.org/10.1107/S0907444912044423 DO - 10.1107/S0907444912044423 ID - Pozharski2013 ER - TY - JOUR AU - Weichenberger, C. X. AU - Pozharski, E. AU - Rupp, B. PY - 2013 DA - 2013// TI - Visualizing ligand molecules in twilight electron density JO - Acta Crystallogr Sect F Struct Biol Cryst Commun VL - 69 UR - https://doi.org/10.1107/S1744309112044387 DO - 10.1107/S1744309112044387 ID - Weichenberger2013 ER - TY - JOUR AU - Berman, H. M. PY - 2000 DA - 2000// TI - The protein data bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Joosten, R. P. AU - Vriend, G. PY - 2007 DA - 2007// TI - PDB improvement starts with data deposition JO - Science (New York, NY) VL - 317 UR - https://doi.org/10.1126/science.317.5835.195 DO - 10.1126/science.317.5835.195 ID - Joosten2007 ER - TY - JOUR AU - Joosten, R. P. AU - Joosten, K. AU - Cohen, S. X. AU - Vriend, G. AU - Perrakis, A. PY - 2011 DA - 2011// TI - Automatic rebuilding and optimization of crystallographic structures in the protein data bank JO - Bioinformatics (Oxford, England) VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr590 DO - 10.1093/bioinformatics/btr590 ID - Joosten2011 ER - TY - JOUR AU - Joosten, R. P. AU - Joosten, K. AU - Murshudov, G. N. AU - Perrakis, A. PY - 2012 DA - 2012// TI - PDB_REDO: constructive validation, more than just looking for errors JO - Acta Crystallographica Section D VL - 68 UR - https://doi.org/10.1107/S0907444911054515 DO - 10.1107/S0907444911054515 ID - Joosten2012 ER - TY - STD TI - The Jython Project. http://www.jython.org/, UR - http://www.jython.org/ ID - ref17 ER - TY - JOUR AU - Hanson, R. M. PY - 2010 DA - 2010// TI - Jmol – a paradigm shift in crystallographic visualization JO - J Appl Cryst VL - 43 UR - https://doi.org/10.1107/S0021889810030256 DO - 10.1107/S0021889810030256 ID - Hanson2010 ER - TY - JOUR AU - Kleywegt, G. J. AU - Harris, M. R. AU - Zou, J. Y. AU - Taylor, T. C. AU - Wählby, A. AU - Jones, T. A. PY - 2004 DA - 2004// TI - The Uppsala electron-density server JO - Acta Crystallogr Sect D Biol Cryst VL - 60 UR - https://doi.org/10.1107/S0907444904013253 DO - 10.1107/S0907444904013253 ID - Kleywegt2004 ER - TY - STD TI - EDS - Uppsala Electron Density Server. http://eds.bmc.uu.se/eds/, UR - http://eds.bmc.uu.se/eds/ ID - ref20 ER - TY - JOUR AU - Magrane, M. PY - 2011 DA - 2011// TI - UniProt Knowledgebase: a hub of integrated protein data JO - Database J Biol Databases Curat VL - 2011 ID - Magrane2011 ER - TY - JOUR AU - Yang, J. AU - Roy, A. AU - Zhang, Y. PY - 2013 DA - 2013// TI - BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks966 DO - 10.1093/nar/gks966 ID - Yang2013 ER - TY - JOUR AU - Edmondson, S. D. AU - Mastracchio, A. AU - Mathvink, R. J. AU - He, J. AU - Harper, B. AU - Park, Y. -. J. AU - Beconi, M. AU - Di Salvo, J. AU - Eiermann, G. J. AU - He, H. AU - Leiting, B. AU - Leone, J. F. AU - Levorse, D. A. AU - Lyons, K. AU - Patel, R. A. AU - Patel, S. B. AU - Petrov, A. AU - Scapin, G. AU - Shang, J. AU - Roy, R. S. AU - Smith, A. AU - Wu, J. K. AU - Xu, S. AU - Zhu, B. AU - Thornberry, N. A. AU - Weber, A. E. PY - 2006 DA - 2006// TI - (2S,3S)-3-Amino-4-(3,3-difluoropyrrolidin-1-yl)-N, N-dimethyl-4-oxo-2-(4-[1,2,4]triazolo[1,5-a]-pyridin-6-ylphenyl)butanamide: a selective alpha-amino amide dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes JO - J Med Chem VL - 49 UR - https://doi.org/10.1021/jm060015t DO - 10.1021/jm060015t ID - Edmondson2006 ER - TY - STD TI - RCSB Protein Data Bank - RCSB PDB - 3Q8W Structure Summary. http://www.rcsb.org/pdb/explore/explore.do?structureId=3Q8W, UR - http://www.rcsb.org/pdb/explore/explore.do?structureId=3Q8W ID - ref24 ER - TY - STD TI - VHELIBS Online Documentation. https://github.com/URVnutrigenomica-CTNS/VHELIBS/wiki, UR - https://github.com/URVnutrigenomica-CTNS/VHELIBS/wiki ID - ref25 ER - TY - JOUR AU - Kleywegt, G. J. AU - Jones, T. A. PY - 1996 DA - 1996// TI - xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets JO - Acta Crystallogr Sect D Biol Cryst VL - 52 UR - https://doi.org/10.1107/S0907444995014983 DO - 10.1107/S0907444995014983 ID - Kleywegt1996 ER - TY - JOUR AU - Tickle, I. J. PY - 2012 DA - 2012// TI - Statistical quality indicators for electron-density maps JO - Acta Crystallogr Sect D Biol Cryst VL - 68 UR - https://doi.org/10.1107/S0907444911035918 DO - 10.1107/S0907444911035918 ID - Tickle2012 ER - TY - JOUR AU - Warren, G. L. AU - Do, T. D. AU - Kelley, B. P. AU - Nicholls, A. AU - Warren, S. D. PY - 2012 DA - 2012// TI - Essential considerations for using protein-ligand structures in drug discovery JO - Drug Discov Today VL - 17 UR - https://doi.org/10.1016/j.drudis.2012.06.011 DO - 10.1016/j.drudis.2012.06.011 ID - Warren2012 ER - TY - STD TI - UniProtKB. http://www.uniprot.org/help/uniprotkb, UR - http://www.uniprot.org/help/uniprotkb ID - ref29 ER - TY - JOUR AU - Winn, M. D. AU - Ballard, C. C. AU - Cowtan, K. D. AU - Dodson, E. J. AU - Emsley, P. AU - Evans, P. R. AU - Keegan, R. M. AU - Krissinel, E. B. AU - Leslie, A. G. W. AU - McCoy, A. AU - McNicholas, S. J. AU - Murshudov, G. N. AU - Pannu, N. S. AU - Potterton, E. A. AU - Powell, H. R. AU - Read, R. J. AU - Vagin, A. AU - Wilson, K. S. PY - 2011 DA - 2011// TI - Overview of the CCP4 suite and current developments JO - Acta Crystallogr Sect D Biol Cryst VL - 67 UR - https://doi.org/10.1107/S0907444910045749 DO - 10.1107/S0907444910045749 ID - Winn2011 ER - TY - BOOK AU - Schrödinger, L. PY - 2010 DA - 2010// TI - The PyMOL Molecular Graphics System ID - Schrödinger2010 ER - TY - JOUR AU - Krieger, E. AU - Koraimann, G. AU - Vriend, G. PY - 2002 DA - 2002// TI - Increasing the precision of comparative models with YASARA NOVA–a self-parameterizing force field JO - Proteins VL - 47 UR - https://doi.org/10.1002/prot.10104 DO - 10.1002/prot.10104 ID - Krieger2002 ER - TY - JOUR AU - Krieger, E. AU - Joo, K. AU - Lee, J. AU - Lee, J. AU - Raman, S. AU - Thompson, J. AU - Tyka, M. AU - Baker, D. AU - Karplus, K. PY - 2009 DA - 2009// TI - Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8 JO - Proteins VL - 77 UR - https://doi.org/10.1002/prot.22570 DO - 10.1002/prot.22570 ID - Krieger2009 ER - TY - JOUR AU - Vos, S. AU - Parry, R. J. AU - Burns, M. R. AU - De Jersey, J. AU - Martin, J. L. PY - 1998 DA - 1998// TI - Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase JO - J Mole Biol VL - 282 UR - https://doi.org/10.1006/jmbi.1998.2051 DO - 10.1006/jmbi.1998.2051 ID - Vos1998 ER - TY - JOUR AU - Hartshorn, M. J. AU - Verdonk, M. L. AU - Chessari, G. AU - Brewerton, S. C. AU - Mooij, W. T. M. AU - Mortenson, P. N. AU - Murray, C. W. PY - 2007 DA - 2007// TI - Diverse, high-quality test set for the validation of protein-ligand docking performance JO - J Med Chem VL - 50 UR - https://doi.org/10.1021/jm061277y DO - 10.1021/jm061277y ID - Hartshorn2007 ER -