Please cite
When you have been using ARP/wARP or/and the ARP/wARP webservice please cite us with the respective publications. Depending on the module(s) you used, select the references given below:
Protein model building
Please cite at least one of the publications below for protein model building
Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular model building for x-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171-1179
Perrakis A, Morris RM, Lamzin VS. (1999) Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463
Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641
Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication:
Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr D Biol Crystallogr. 67, 355-367
ARPEM - ARP/wARP model building for electron microscopy
Chojnowski G, Heuser P, Lamzin VS (2018), A dedicated paper, describing the method is under preparartion
Until the dedicated paper is published please cite:
Chojnowski G, Heuser P, Lamzin VS (2018), ARPEM - ARP/wARP model building for electron microscopy over the web, arpwarp.embl-hamburg.de
Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular model building for x-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171-1179
Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication:
Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr D Biol Crystallogr. 67, 355-367
Nucleotides
Please cite the publication below for nucleotide model building
Hattne J, Lamzin VS. (2008) Pattern recognition-based detection of planar objects in 3D electron density maps. Acta Crystallogr D Biol Crystallogr. 64, 834-842
Solvent modelling
Please cite at least one of the publications below for solvent modelling with ARP/wARP
Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147
Lamzin VS, Perrakis A, Wilson KS. (2001) The ARP/WARP suite for automated construction and refinement of protein models. In Int. Tables for Crystallography. Vol. F: Crystallography of biological macromolecules (Rossmann MG, Arnold E, eds.), Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 720-722
Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication:
Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr D Biol Crystallogr. 67, 355-367
Ligand building
Please cite at least one of the publications below for ligand building with ARP/wARP
Carolan CG, Lamzin VS. (2014) Automated identification of crystallographic ligands using sparse-density representations. Acta Crystallogr D Biol Crystallogr. 70, 1844-1853
Langer GG, Evrard GX, Carolan CG, Lamzin VS. (2012) Fragmentation-tree density representation for crystallographic modelling of bound ligands. J Mol Biol. 419, 211-222
Secondary Structure Building Quickfold
Please cite the publication below for Quickfold
Langer G, Cohen SX, Lamzin VS, Perrakis A. (2008) Automated macromolecular model building for x-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171-1179
Dipcheck
Please cite the publication below for Dipcheck
Pereira J, Lamzin VS. A distance geometry-based description and validation of protein main-chain conformation. IUCrJ (2017) 4, 657-670.