title: ProteinShop: a tool for interactive protein manipulation and steering.
abstract: 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. Last, 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.
authors.affiliation: Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. SNCrivelli@lbl.gov
authors.forename: Silvia
authors.initials: S
authors.lastname: Crivelli
authors.forename: Oliver
authors.initials: O
authors.lastname: Kreylos
authors.forename: Bernd
authors.initials: B
authors.lastname: Hamann
authors.forename: Nelson
authors.initials: N
authors.lastname: Max
authors.forename: Wes
authors.initials: W
authors.lastname: Bethel
mesh_terms: D019295:Computational Biology; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins