ProteinShop: A tool for interactive protein manipulation and steering

Silvia Crivelli, Oliver Kreylos, Bernd Hamann, Nelson Max, Wes Bethel
2004 Journal of Computer-Aided Molecular Design  
We describe ProteinShop, a new visualization tool that streamlines and simplifies the process of determining optimal protein folds. ProteinShop may be used at different stages of a protein structure prediction process. First, it can create protein configurations containing secondary structures specified by the user. Second, it can interactively manipulate protein fragments to achieve desired folds by adjusting the dihedral angles of selected coil regions using an Inverse Kinematics method.
more » ... it serves as a visual framework to monitor and steer a protein structure prediction process that may be running on a remote machine. ProteinShop was used to create initial configurations for a protein structure prediction method developed by a team that competed in CASP5. ProteinShop's use accelerated the process of generating initial configurations, reducing the time required from days to hours. This paper describes the structure of ProteinShop and discusses its main features. configurations [1] . This method begins with the extended sequence of amino acids and builds secondary structures through local minimizations with soft constraints. Because proteins have thousands of atoms, these local optimizations may take hours or even days to converge. The problem is compounded by the presence of β-strands for which there is a combinatorial number of possible strand alignments, each of which needs to be created with a different constrained minimization. ProteinShop allows a scientist to significantly reduce the time to create a set of structures to a matter of hours. This fact is a significant achievement. Furthermore, protein structure simulation programs based on energy minimization principles typically were executed in "batch mode," where it was not possible to observe or guide the evolution of the optimization process. ProteinShop makes it possible, when used in combination with an optimization system, to interact with and guide the numerical optimization process. In summary, ProteinShop substantially reduces set-up times for initial protein configurations and allows us to effectively monitor and interact with the optimization process, which allows us in turn to obtain in reduced time significantly better results than with existing methods. Although several packages exist that can display protein structures [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] , they do not provide support for the interactive manipulation of protein structures and their subsequent minimization. Among the most well-known packages are RasMol and its derivative Protein Explorer,
doi:10.1023/b:jcam.0000046822.54719.4f pmid:15562991 fatcat:shma2duprfayneokkpvs2k26wm