Acknowledging MAX IV
MAX IV has a number of policies governing user access. If you are unsure about any aspect, please consult the User Policies page or contact the MAX IV User Office for further information.
In accordance with MAX IV User Policies, it is mandatory to acknowledge MAX IV and its funders in all publications and other material arising from work carried out at the facility.
Please follow this link for details on the required acknowledgement: User Policies page.
Acknowledging FragMAX & BioMAX
Please check out Acknowledgement and References in the Macromolecular Crystallography section.
Automated pipelines for data processing
Please check out Acknowledgement and References in the Macromolecular Crystallography section.
Software
X-ray data processing and analysis at FragMAX rely on a range of established and widely used software tools. We kindly ask that you cite the appropriate sources when making use of these tools in your work.
Data processing
XDS
Kabsch, W., 2010. XDS. Acta Cryst D 66, 125–132. https://doi.org/10.1107/S0907444909047337
Pointless, Aimless
Evans, P.R., Murshudov, G.N., 2013. How good are my data and what is the resolution? Acta Cryst D 69, 1204–1214. https://doi.org/10.1107/S0907444913000061
autoPROC
Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O., Paciorek, W., Womack, T. & Bricogne, G. (2011). Data processing and analysis with the autoPROC toolbox. Acta Cryst. D67, 293-302.
FragMAXapp
Lima, G.M.A., Jagudin, E., Talibov, V.O., Benz, L.S., Marullo, C., Barthel, T., Wollenhaupt, J., Weiss, M.S., Mueller, U., 2021. FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Cryst D 77. https://doi.org/10.1107/S2059798321003818
Initial refinement
Refmac
Murshudov, G.N., Vagin, A.A., Dodson, E.J., 1997. Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst D 53, 240–255. https://doi.org/10.1107/S0907444996012255
Dimple
Wojdyr, M., Keegan, R., Winter, G., Ashton, A. (2013) DIMPLE – a pipeline for the rapid generation of difference maps from protein crystals with putatively bound ligands. Acta Cryst. A69: s299
Ligand restraints
ACEDRG
Long, F., Nicholls, R.A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A., Murshudov, G.N., 2017. AceDRG: a stereochemical description generator for ligands. Acta Cryst D 73, 112–122. https://doi.org/10.1107/S2059798317000067
Hit finding
PanDDA
Pearce, N.M., Krojer, T., Bradley, A.R., Collins, P., Nowak, R.P., Talon, R., Marsden, B.D., Kelm, S., Shi, J., Deane, C.M., Von Delft, F., 2017. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nature Communications 8.
Cluster4x
Ginn, H.M., 2020. Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis. Acta Cryst D 76, 1134–1144. https://doi.org/10.1107/S2059798320012619
General
Agirre, J. et al. The CCP4 suite: integrative software for macromolecular crystallography. Acta Cryst D 79, 449–461 (2023).
Fragment libraries
FragMAXlib library
Lima, G.M.A., Talibov, V.O., Jagudin, E., Sele, C., Nyblom, M., Knecht, W., Logan, D.T., Sjögren, T., Mueller, U., 2020. FragMAX: the fragment-screening platform at the MAX IV Laboratory. Acta Cryst D 76, 771–777. https://doi.org/10.1107/S205979832000889X
DSI-poised library
Cox, O.B., Krojer, T., Collins, P., Monteiro, O., Talon, R., Bradley, A., Fedorov, O., Amin, J., Marsden, B.D., Spencer, J., Delft, F. von, Brennan, P.E., 2016. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322–2330. https://doi.org/10.1039/C5SC03115J
EU Openscreen library
Jalencas, X., Berg, H., Espeland, L.O., Sreeramulu, S., Kinnen, F., Richter, C., Georgiou, C., Yadrykhinsky, V., Specker, E., Jaudzems, K., Miletić, T., Harmel, R., Gribbon, P., Schwalbe, H., Brenk, R., Jirgensons, A., Zaliani, A., Mestres, J., 2024. Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. RSC Med. Chem. https://doi.org/10.1039/D3MD00724C
MiniFrag library
O’Reilly, M., Cleasby, A., Davies, T.G., Hall, R.J., Ludlow, R.F., Murray, C.W., Tisi, D., Jhoti, H., 2019. Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design. Drug Discovery Today. https://doi.org/10.1016/j.drudis.2019.03.009