Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

2008 | Gerrit G Langer, Serge X Cohen, Victor S Lamzin, and Anastassis Perrakis
ARP/wARP version 7 is a software suite for automated macromolecular model building in X-ray crystallography. It enables the automatic generation of macromolecular models from electron density maps, with a reproducible computational procedure. The software performs several tasks, including iterative protein model building, secondary structure construction, flexible loop building, ligand placement, and water molecule identification. It is user-friendly, with a graphical user interface or command line, and can be used by non-experts. The time required is typically a few minutes, though iterative model building may take several hours. ARP/wARP has been widely used in structural genomics and studies of complex macromolecular assemblies and membrane proteins. It is often used as a benchmark to evaluate the quality of electron density maps. The software is integrated into many automated crystallography pipelines as the default model building engine. ARP/wARP's main chain tracing uses all available atoms of the hybrid model as potential Cα atoms. Peptides between potential Cα pairs are recognized by matching the electron density surrounding each pair to that precomputed for true Cα pairs. The recognized peptides are then assembled into linear polypeptide chain fragments using a graph search algorithm. Side chains are docked in sequence with side chains built in the best rotamer configuration and refined in real space. Loop building identifies missing parts of the model and constructs likely conformations. Secondary structure recognition is used at lower resolutions to build protein helices and strands. Ligand building involves modeling bound ligands in the difference electron density map. The software identifies regions of difference density and produces an ensemble of putative ligand structures to best fit the local density. The best model is selected after refinement. Cocktail screening distinguishes compounds from a list of ligand candidates based on their shapes. Solvent building constructs a solvent structure in a difference electron density map. The protein part of the model is not rebuilt, and solvent molecules are placed around the protein. The procedure is iterative, and model building and refinement are linked into a unified process. ARP/wARP is used in both 'Classic' and 'Expert System' interfaces. The 'Classic' interface is used for automated model building, while the 'Expert System' interface allows for more complex tasks. The software is available for Linux, Mac OSX, and other platforms. It is freely available for academic use and can be downloaded from its website. The software is used in a variety of applications, including structural genomics, protein-ligand complex studies, and membrane protein research. It has been tested on thousands of protein-ligand complexes and has a high success rate in ligand building. The software is also used in automated crystallography pipelines and is integrated with the CCP4 program suite. The software is designed to work at resolutions down to 4.5 Å and can produce complete models at resolutions as low as 2.7 Å. It is efficient and can complete model building in a few minutesARP/wARP version 7 is a software suite for automated macromolecular model building in X-ray crystallography. It enables the automatic generation of macromolecular models from electron density maps, with a reproducible computational procedure. The software performs several tasks, including iterative protein model building, secondary structure construction, flexible loop building, ligand placement, and water molecule identification. It is user-friendly, with a graphical user interface or command line, and can be used by non-experts. The time required is typically a few minutes, though iterative model building may take several hours. ARP/wARP has been widely used in structural genomics and studies of complex macromolecular assemblies and membrane proteins. It is often used as a benchmark to evaluate the quality of electron density maps. The software is integrated into many automated crystallography pipelines as the default model building engine. ARP/wARP's main chain tracing uses all available atoms of the hybrid model as potential Cα atoms. Peptides between potential Cα pairs are recognized by matching the electron density surrounding each pair to that precomputed for true Cα pairs. The recognized peptides are then assembled into linear polypeptide chain fragments using a graph search algorithm. Side chains are docked in sequence with side chains built in the best rotamer configuration and refined in real space. Loop building identifies missing parts of the model and constructs likely conformations. Secondary structure recognition is used at lower resolutions to build protein helices and strands. Ligand building involves modeling bound ligands in the difference electron density map. The software identifies regions of difference density and produces an ensemble of putative ligand structures to best fit the local density. The best model is selected after refinement. Cocktail screening distinguishes compounds from a list of ligand candidates based on their shapes. Solvent building constructs a solvent structure in a difference electron density map. The protein part of the model is not rebuilt, and solvent molecules are placed around the protein. The procedure is iterative, and model building and refinement are linked into a unified process. ARP/wARP is used in both 'Classic' and 'Expert System' interfaces. The 'Classic' interface is used for automated model building, while the 'Expert System' interface allows for more complex tasks. The software is available for Linux, Mac OSX, and other platforms. It is freely available for academic use and can be downloaded from its website. The software is used in a variety of applications, including structural genomics, protein-ligand complex studies, and membrane protein research. It has been tested on thousands of protein-ligand complexes and has a high success rate in ligand building. The software is also used in automated crystallography pipelines and is integrated with the CCP4 program suite. The software is designed to work at resolutions down to 4.5 Å and can produce complete models at resolutions as low as 2.7 Å. It is efficient and can complete model building in a few minutes
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[slides and audio] Automated macromolecular model building for X-ray crystallography using ARP%2FwARP version 7