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
Chojnowski G, Pereira J and Lamzin VS. (2019) Sequence assignment for low-resolution modelling of protein crystal structures. Acta Crystallogr D Struct Biol. 75, 753-763
Chojnowski G., Choudhury K., Heuser P., Sobolev E., Pereira J., Oezugurel U. and Lamzin VS. (2020) The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution Acta Crystallogr D Struct Biol. 76, 248-260
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, Pereira J and Lamzin VS. (2019) Sequence assignment for low-resolution modelling of protein crystal structures. Acta Crystallogr D Struct Biol. 75, 753-763
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.