Automation molecular replacement

Out of the work with HT-XPIPE it became clear to the consortium that there was a need to expand the automated molecular replacement protocol embodied in HT-XPIPE to handle scenarios in which either the target was a new project or ligand-binding caused a packing change in the protein that... 

Qaude, J. B., Suhre, K., Notredame, C., Qaverie, J. M., and Abergel, C. (2004) CaspR a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32, W606-609. 

Kissinger, C. R., GeUtaar, D. K., and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D 55, 4844 91. 

Navaza, J. and Saludjian, P. (1997) AmoRe an automated molecular replacement package. Method Enzymol. T7k, 581-594. 

Navaza J. AMORE—an automated package for molecular replacement. Acta Cryst. 1994 A50 157-63. 

Keegan, R. M. and Wynn, M. D. (2007) Automated search-model discovery and preparation for structure solution by molecular replacement. Actu Crystallogr. D 63, 447-457. 

Vagin, A. and Teplyakov, A. (1997) MOLREP an automated program for molecular replacement.. Appl. Crystallogr. 30,1022-1025. 

Structure-based drug discovery involves determination of many cocrystal structures with different ligands bound to the same target protein. In such cases, where the structure of the protein is well known, automated structure determination procedures rely on molecular replacement to supply the... 

Molecular replacement is usually straightforward and performed within minutes. However, when only low resolution data and a poor search model are available, model bias can become an issue and experimental phasing may be needed. Nevertheless, the molecular replacement method is extremely useful in the context of structure-based design where it is used to expedite the determination of multiple protein complexes or to analyze, in an automated way, multiple data sets from a fragment-based screen. 

Once a first electron-density map is obtained, it is interpreted by the crystallographer. In the case of a MIR(AS) map, a complete model of the protein has to be fitted to the electron density. The Ca atoms are placed first (chain tracing), and subsequently the complete main chain and the side chains are built, a process which has become more and more automated in recent years, notably when high resolution data are available. In the case of molecular replacement, the search model needs to be updated to reflect the molecule present in the crystal. The model is usually of a similar protein and the changes involve the substitution of some amino acids, the introduction of insertions and deletions, the modification of some loops, and so on. 

Vagin A, Teplyakov A An automated program for molecular replacement. J... 

The applicability of such VS in combination with tools available include situations where portions of any molecule need replacement with bioisosteric fragments. In this regard, BROOD software [105] and MOE [222] provide automated tools for fragment removal, replacement, and minimization to relieve any strain in the molecular assembly step and provide a database of fragments(isosteres) that could be enhanced in custom fashion by an enterprise as well. These software allow facile FBVS in 3D. Since this software has become available within the last 2 years, there seem to be a dearth of use cases in the published literature. However, anecdotal reports indicate that these are being used regularly in industry and the Websites of these two vendors provide adequate information for the inquisitive reader. 

The breakthrough in peptide chemistry, which opened up applications in biochemistry and molecular biology, was the development of solid phase synthesis by Merrifield in 1963. This formed the basis of automated synthetic procedures in which the nascent peptide chain was covalently linked to a solid support such as a styrene-divinylbenzene copolymer the complex isolation and purification procedures needed to separate reactants and products at the end of each reaction cycle, which characterised previous solution methods of peptide synthesis, were replaced by a simple washing step. With modern automated methods of peptide synthesis, the time for an Fmoc reaction cycle has been reduced to 20 min, so that a 50-residue peptide can be synthesised in a day (Chan and White 2000). 

---