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ARP/wARP
Welome to the ARP/wARP webservice for Crystallographic Macromolecular Model Building. Builds proteins, RNA/DNA, secondary structure, side chains, loops, solvent and ligands.

Please note that the use of this service requires you to consent to the conditions and license agreements as well as in the disclaimer. Also, please do not forget to cite the publications as given in the log files of each job..
Model Building - Phase Mode
Classic ARP/wARP Modelbuilding starting from resonable initial phases. Given appropriate quality of the phases, this should build >95% of the molecule at 2.5 Å and better resolution. It is also applicable with reduced performance down to 3.5 Å resolution

Required:
MTZ-File with FP/SIGFP, PHI and FOM
Optional:
Sequence
Model Building - Model Mode
Classic ARP/wARP Modelbuilding starting from known/homologous model of the target struture. Given appropriate quality of the model, this should build >95% of the molecule at 2.5 Å and better resolution. It is also applicable with reduced performance down to 3.5 Å resolution

Required:
MTZ-File with FP/SIGFP
PDB-File with the coordinates of the initial model
Optional:
Sequence
Phaserestrains
SAD-refinement
Model Building - Electron Microscopy
Soon here!

Required:
Optional:
Quickfold - Secondary Structure Tracing
Quickfold performs a rapid model building for secondary structure elements. Quickfold has been designed to work down to 4.5 Å resolution.

Required:
MTZ-File with FP/SIGFP, PHI and FOM
Optional:
Nucleotides - Model Building for DNA/RNA
This module builds fragments of DNA or RNA. The input is an MTZ file containing the phases from which the map best describing the nucleotide region can be computed. The produced poly-nucleotides are quite accurate, a typical r.m.s.d. for the built backbone atoms is 0.6 Å with X-ray data extending to around 3.0 Å resolution. The method is not sensitive to a particular DNA or RNA conformation.

Required:
MTZ-File with FP/SIGFP, PHI and FOM
Optional:
Solvent Modelling
Within solvent building module restrained reciprocal space refinement is carried out with REFMAC while ARP/wARP is performing automatic adjustment of the solvent structure. Resolution of the data should be 3 Å or higher. The output is the protein model with the solvent molecules transformed with symmetry operations to lie around the protein.

Required:MTZ-File with FP/SIGFP
PDB-File with the coordinates of the initial model

Optional:
Ligands
ARP/wARP can built a model of a ligand into the density map. The ARP/ wARP ligand building module requires the X-ray data (in MTZ format), the built protein without ligands (in PDB format) and either a template model of the ligand to build (also in PDB format) or a ligand 3-letter code.

Required:
MTZ-File
PDB-File of the protein
Optional:
PDB-File of Ligand
Dipcheck Validation
Validation of protein models using dipcheck service (http://www.embl-hamburg.de/dipcheck/).

Required: PDB File
Ligands by ViCi
ViCi is an ARP/wARP independent webservice provided by the Lamzin Group for ligand-based drug design. ViCi uses a combination of mathematical descriptors of molecular size, shape and topology to describe small molecule structures. Following input of a template molecule, the software will rapidly screen a database (currently 8 million compounds) and extract those predicted to have similar shape and electrostatic compositions and therefore to be possible ligands for the same protein. (http://www.embl-hamburg.de/vici/).

Required: Ligand file as PDB
Autorickshaw
The automated crystal structure determination platform is a system which contains several distinct decision-makers which executes a number of macromolecular crystallographic software programs to produce a software pipeline for automated and efficient crystal structure determination. A large number of possible structure solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. At the end the model is built with ARP/wARP (http://www.embl-hamburg.de/Auto-Rickshaw/).

Balbes @ CCP4
An automated Molecular Replacement (MR) pipeline - Balbes integrates into one system all the components necessary for solving a crystal structure by Molecular Replacement. Balbes is part of the ccp4 online services and at the end the model is built with ARP/wARP (https://www.ccp4.ac.uk/ccp4online/).

Please cite:
Langer G, Cohen SX, Lamzin VS, Perrakis A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. (2008) Nat Protoc. 3, 1171-1179.