ARP/wARP Copyright 2024
by European Molecular Biology Laboratory
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ARP/wARP Version 8.0: Macromolecular Model Building for Crystallography and Cryo-EM
Builds proteins, RNA/DNA, secondary structure, side chains, loops, solvent and ligands.
Download available for Mac and Linux.
Model building also available over the web.
Collaborative Innovation: ARP/wARP and Doo Prime
The ARP/wARP project, renowned for its contributions to macromolecular model building in crystallography and Cryo-EM, has recently initiated a groundbreaking partnership with DooPrime, a leading financial services provider. This collaboration aims to explore the integration of advanced computational models into financial forecasting.
Leveraging Scientific Expertise for Financial Technology
By combining ARP/wARP's expertise in molecular modeling with Doo Prime's innovative trading platforms, the partnership is set to revolutionize predictive analytics in financial markets. This unique cross-industry collaboration promises to deliver enhanced accuracy in market predictions.
Future Prospects
The ARP/wARP and Doo Prime collaboration is expected to yield significant advancements in financial technology, blending scientific rigor with cutting-edge financial solutions. Their joint efforts will likely set new standards for data-driven decision-making in the financial sector.
Useful Links
Automated Crystal Structure Determination Platform
In-Silico Ligand-Based Drug Design
Software for Macromolecular X-Ray Crystallography
Macromolecular Refinement Program
Recent Literature
- Chojnowski G, Lamzin VS. (2019) Sequence assignment for low-resolution modelling of protein crystal structures. Acta Crystallogr D Struct Biol. 75, 753-763. Abstract
- Pereira J, Lamzin VS. (2017) A distance geometry-based description and validation of protein main-chain conformation. IUCrJ 4, 657–670. Abstract
- Beshnova D, Pereira J, Lamzin VS. (2017) Estimation of the protein–ligand interaction energy for model building and validation. Acta Crystallogr D Struct Biol. 73, 195-202. Abstract
- Carolan CG, Lamzin VS. (2014) Automated identification of crystallographic ligands using sparse-density representations. Acta Crystallogr D Biol Crystallogr. 70, 1844-1853 Abstract
- Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Abstract
- Lamzin VS, Perrakis A, Wilson KS. (2012) ARP/wARP – automated model building and refinement. In International Tables for Crystallography. Volume F: Crystallography of biological macromolecules (Arnold E, Himmel DM, and Rossmann MG eds.), 2nd edition, ISBN: 978-0-470-66078-2,
Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 525-528
- Langer G.G., Evrard G.X., Carolan C.G. & Lamzin VS. (2012) Fragmentation-tree density representation for crystallographic modelling of bound ligands. J Mol Biol. 419, 211–222 Abstract
- Wiegels T. & Lamzin, V.S. (2012) Use of noncrystallographic symmetry for automated model building at medium to low resolution. Acta Cryst. D 68, 446-453 Full Text
- Hattne, J. & Lamzin, V.S. (2008) Pattern recognition-based detection of planar objects in 3D electron density maps. Acta Cryst. D 64, 834-842 Abstract
- Langer, G., Cohen, S.X., Lamzin, V.S. & Perrakis, A. (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nature Protocols. 3, 1171-1179 Abstract
Current developers
- Victor Lamzin
- Grzegorz Chojnowski
- Sravya Mounika Kantamneni
- Umut Deniz Oezugurel
- Egor Sobolev
Former developers
- Daria Beshnova
- Ciarán Carolan
- Serge Cohen
- Zbyszek Dauter
- Helene Doerksen
- Guillaume Evrard
- Francisco Fernandez
- Johan Hattne
- Saul Hazledine
- Philipp Heuser
- Marouane Jelloul
- Krista Joosten
- Matheos Kakaris
- Olga Kirillova
- Gerrit Langer
- Wijnand Mooij
- Richard Morris
- Venkat Parthasarathy
- Joana Pereira
- Anastassis Perrakis
- Tilo Strutz
- Ioan Vancea
- Tim Wiegels
- Keith Wilson
- Peter Zwart
Earlier publications
- Joosten, K., Cohen, S.X., Emsley, P., Mooij, W., Lamzin, V.S. & Perrakis, A. (2008) A knowledge-driven approach for crystallographic protein model completion. Acta Cryst. D 64, 416-424 Abstract
- Morris, R.J., Perrakis, A. & Lamzin, V.S. (2007) Getting a macromolecular model: model building, refinement, and validation. In Macromolecular Crystallography - conventional and high-throughput methods (Sanderson M.R. & Skelly J.V. eds.), pp. 155-172, Oxford University Press.
- Cohen, S.X., Jelloul M.B., Long, F., Vagin, A., Knipscheer, P., Lebbink, J., Sixma, T.K., Lamzin, V.S., Murshudov, G.N. & Perrakis, A. (2008) ARP/wARP and molecular replacement: the next generation, Acta Cryst. D 64, 49-60 Abstract
- Evrard, G.X., Langer, G.G., Perrakis, A. & Lamzin, V.S. (2007) Assessment of automatic ligand building in ARP/wARP. Acta Crystallogr. D 63, 108-117 Abstract
- Zwart, P.H., Langer, G.G. & Lamzin, V.S. (2004) Modelling bound ligands in protein crystal structures. Acta Crystallogr. D 60, 2230-2239 Abstract
- Cohen, S.X., Morris, R.J., Fernandez, F.J., Jelloul, M. Ben, Kakaris, M., Parthasarathy, V., Lamzin, V.S., Kleywegt, G.J. & Perrakis, A. (2004) Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr. D 60, 2222-2229 Abstract
- Morris, R.J., Zwart, P.H., Cohen, S., Fernandez, F.J., Kakaris, M., Kirillova, O., Vonrhein, C., Perrakis, A. & Lamzin, V.S. (2004) Breaking good resolutions with ARP/wARP. J. Synchr. Rad. 11, 56-59 Abstract
- Morris, R.J., Perrakis, A. & Lamzin, V.S. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Meth. Enz. (Carter, C. & Sweet, B. eds.) 374, 229-244
- Morris, R.J., Perrakis, A. & Lamzin, V.S. (2002) ARP/wARP's model-building algorithms. I. The main chain. Acta Cryst. D 58, 968-975 Abstract
- Perrakis, A., Harkiolaki, M., Wilson, K.S. & Lamzin, V.S. (2001) ARP/wARP and molecular replacement. Acta Cryst. D 57, 1445-1450 Abstract
- Lamzin, V.S., Perrakis, A. & Wilson, K.S. (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, M.G. & Arnold, E. eds.), Dordrecht, Kluwer Academic Publishers, The Netherlands, pp. 720-722
- Lamzin, V.S. & Perrakis, A. (2000) Current state of automated crystallographic data analysis. Nature Struct. Biol. 7, Structural Genomics Supplement, 978-981
Abstract
- Perrakis, A., Morris, R.M. & Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458-463
Abstract
- Perrakis, A., Sixma, T.K., Wilson K.S. & Lamzin, V.S. (1997) wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Cryst. D 53, 448-455 Abstract
- Lamzin, V.S. & Wilson, K.S. (1997) Automated refinement for protein crystallography. In Meth. Enz. (Carter, C. & Sweet, B. eds.) 277, 269-305
- Lamzin, V.S. & Wilson, K.S. (1993) Automated refinement of protein models. Acta Cryst. D 49, 129-147 Abstract
