./arp_easy/templates/plain_pages/citeme.html ARP/wARP - FAQ

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

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

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

ARPEM - ARP/wARP model building for electron microscopy

Chojnowski G, Sobolev E, Heuser P and Lamzin VS. (2021). The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP. Acta Crystallogr D Struct Biol. 77(2).


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.

Thank you!