THIS FILE CONTAINS ALL REFERENCES ASSOCIATED WITH AMPLE.

WHEN ADDING AN ENTRY, PLEASE ENSURE THAT YOU PROVIDE THE FOLLOWING KEYWORDS
author, doi, journal, number, pages, title, volume, year, label
YOU CAN ADD FURTHER KEYWORDS, BUT THE ABOVE ARE ESSENTIAL.

@article{Bibby2012,
   author = {Bibby, Jaclyn and Keegan, Ronan M. and Mayans, Olga and Winn, Martyn D. and Rigden, Daniel J.},
   doi = {10.1107/S0907444912039194},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {AMPLE},
   number = {12},
   pages = {1622--1631},
   title = {{AMPLE: A cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models}},
   volume = {68},
   year = {2012},
}

@article{Bibby2013,
   author = {Bibby, Jaclyn and Keegan, Ronan M. and Mayans, Olga and Winn, Martyn D. and Rigden, Daniel J.},
   doi = {10.1107/S0907444913018453},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {AMPLE_NMR},
   number = {11},
   pages = {2194--2201},
   title = {{Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement}},
   volume = {69},
   year = {2013},
}

@article{Keegan2015,
   author = {Keegan, Ronan M. and Bibby, Jaclyn and Thomas, Jens M. H. and Xu, Dong and Zhang, Yang and Mayans, Olga and Winn, Martyn D. and Rigden, Daniel J.},
   doi = {10.1107/S1399004714025784},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {AMPLE_MODELLING},
   number = {2},
   pages = {338--343},
   title = {{Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models}},
   volume = {71},
   year = {2015},
}

@article{Thomas2015,
   author = {Thomas, Jens M. H. and Keegan, Ronan M. and Bibby, Jaclyn and Winn, Martyn D. and Mayans, Olga and Rigden, Daniel J.},
   doi = {10.1107/S2052252515002080},
   journal = {IUCrJ},
   label = {AMPLE_COILS},
   number = {2},
   pages = {198--206},
   title = {{Routine phasing of coiled-coil protein crystal structures with AMPLE}},
   volume = {2},
   year = {2015},
}

@article{Simkovic2016,
   author = {Simkovic, Felix and Thomas, Jens M. H. and Keegan, Ronan M. and Winn, Martyn D. and Mayans, Olga and Rigden, Daniel J.},
   doi = {10.1107/S2052252516008113},
   journal = {IUCrJ},
   label = {AMPLE_CONTACTS},
   number = {4},
   pages = {259--270},
   title = {{Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds}},
   volume = {3},
   year = {2016},
}

===============================================
BELOW ARE ALL CITATIONS FOR ADDITIONAL PROGRAMS
===============================================

@article{Murshudov1997,
   author = {Murshudov, Garib N. and Vagin, Alexei A. and Dodson, Eleanor J.},
   doi = {10.1107/S0907444996012255},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {REFMAC},
   number = {3},
   pages = {240--255},
   title = {{Refinement of macromolecular structures by the maximum-likelihood method}},
   volume = {53},
   year = {1997},
}


@article{Zhang2004,
   author = {Zhang, Yang and Skolnick, Jeffrey},
   doi = {10.1002/jcc.20011},
   journal = {Journal of Computational Chemistry},
   label = {SPICKER},
   number = {6},
   pages = {865--871},
   title = {{SPICKER: A clustering approach to identify near-native protein folds}},
   volume = {25},
   year = {2004},
}

@article{Cowtan2006,
   author = "Cowtan, Kevin",
   doi = {10.1107/S0907444906022116},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {Buccaneer},
   number = {9},
   pages = {1002--1011},
   title = {{The Buccaneer software for automated model building. 1. Tracing protein chains}},
   volume = {62},
   year = {2006},
}


@article{Theobald2006,
   author = {Theobald, Douglas L. and Wuttke, Deborah S.},
   doi = {10.1093/bioinformatics/btl332},
   journal = {Bioinformatics},
   label = {THESEUS},
   number = {17},
   pages = {2171-2172},
   title = {{THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures}},
   volume = {22},
   year = {2006},
}

@article{McCoy2007,
   author = {McCoy, Airlie J. and Grosse-Kunstleve, Ralf W. and Adams, Paul D. and Winn, Martyn D. and Storoni, Laurent C. and Read, Randy J.},
   doi = {10.1107/S0021889807021206},
   journal = {J. Appl. Cryst.},
   label = {Phaser},
   number = {4},
   pages = {658--674},
   title = {{Phaser crystallographic software}},
   volume = {40},
   year = {2007},
}


@article{Cohen2008,
   author = {Cohen, Serge X. and Ben Jelloul, Marouane and Long, Fei and Vagin, Alexei and Knipscheer, Puck and Lebbink, Joyce and Sixma, Titia K. and Lamzin, Victor S. and Murshudov, Garib N. and Perrakis, Anastassis},
   doi = {10.1107/S0907444907047580},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {Arp_Warp},
   number = {1},
   pages = {49--60},
   title = {{ARP/wARP and molecular replacement: the next generation}},
   volume = {64},
   year = {2008},
}

@article{Keegan2008,
   author = {Keegan, Ronan M. and Winn, Martyn D.},
   doi = {10.1107/S0907444907037195},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {MrBUMP},
   number = {1},
   pages = {119--124},
   title = {{MrBUMP: an automated pipeline for molecular replacement}},
   volume = {64},
   year = {2008},
}

@article {Krivov2009,
   author = {Krivov, Georgii G. and Shapovalov, Maxim V. and Dunbrack, Roland L.},
   doi = {10.1002/prot.22488},
   journal = {Proteins: Struct., Funct., Bioinf.},
   label = {SCWRL4},
   number = {4},
   pages = {778--795},
   title = {{Improved prediction of protein side-chain conformations with SCWRL4}},
   volume = {77},
   year = {2009},
}

@article{Sheldrick2010,
   author = {Sheldrick, George M.},
   doi = {10.1107/S0907444909038360},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {SHELXE},
   number = {4},
   pages = {479--485},
   title = {{Experimental phasing with SHELXC/D/E: combining chain tracing with density modification}},
   volume = {66},
   year = {2010},
}

@article{Vagin2010,
   author = {Vagin, Alexei A and Teplyakov, Alexei},
   doi = {10.1107/S0907444909042589},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {Molrep},
   number = {1},
   pages = {22--25},
   title = {{Molecular replacement with MOLREP}},
   volume = {66},
   year = {2010},
}

@article{Winn2011,
   author = {Winn, Martyn D. and Ballard, Charles C. and Cowtan, Kevin D. and Dodson, Eleanor J. and Emsley, Paul and Evans, Phil R. and Keegan, Ronan M. and Krissinel, Eugene B. and Leslie, Andrew G. W. and McCoy, Airlie and McNicholas, Stuart J. and Murshudov, Garib N. and Pannu, Navraj S. and Potterton, Elizabeth A. and Powell, Harold R. and Read, Randy J. and Vagin, Alexei and Wilson, Keith S.},
   doi = {10.1107/S0907444910045749},
   journal = "Acta Crystallographica Section D",
   label = {CCP4},
   number = {4},
   pages = {235--242},
   title = {{Overview of the CCP4 suite and current developments}},
   volume = {67},
   year = {2011},
}

@article{Thorn2014,
   author = {Thorn, Andrea and Sheldrick, George M.},
   doi = {10.1107/S0907444913027534},
   journal = {Acta Crystallogr. Sect. D Biol. Crystallogr.},
   label = {SHELXE},
   number = {11},
   pages = {2251--2256},
   title = {{Extending molecular-replacement solutions with SHELXE}},
   volume = {69},
   year = {2013},
}

@article{Hung2014,
   author = {Hung, Ling-Hong and Samudrala, Ram},
   doi = {10.1093/bioinformatics/btu098},
   journal = {Bioinformatics},
   label = {FPC},
   number = {12},
   pages = {1774--1776},
   title = {fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data},
   volume = {30},
   year = {2014},
}