Protein Design is a versatile application for modeling and analyzing protein structures. There are two major palettes associated with this application, Protein Design and Protein Utilities. The Protein Design palette contains 18 options that can be classified into three types of utilities. The Protein Utilities palette is also displayed and contains visual tools and structure checks, using the Protein Health option.
This reference book is designed to give a general description of each of the utility interfaces listed above including the scientific methods, and options and tools. The information is arranged in alphabetical order by palettes.
A variety of options are available for aligning sequences, identifying homologous regions, and superpositioning structures.
Protein Design uses geometric relations between secondary structural elements to automatically identify domains, and provides tools that allow you to define and edit the domains.
This utility provides tools that assign secondary structures to proteins. By defining the secondary structure of a molecule, the shape of the molecule can be visualized. This is a two-step procedure, wherein hydrogen bonds are calculated, then secondary structures are assigned based on those hydrogen bond patterns and phi/psi angles.
The tools in this utility determine the solvent accessibility of a molecule or the contact area between molecules or regions of molecules.
This utility enables you to copy coordinates from a known structure or structures to a sequence whose structure is unknown.
The most common use of contact maps is to show the inter-residue Ca-Ca distances. Similar properties which are a function of two residues could also be plotted in similar fashion, such as inter-residue VDW energy or number of inter-residue hydrogen bonds. The properties currently displayed as contact maps in this utility are: Ca-Ca distances; Cb-Cb and side chain contact distances; van der Waals interaction energy; electrostatic interaction energy; total interaction energy; hydrogen bonds; and residue type interactions.
The protein editor provides tools to modify the sequence of a protein by mutating, inserting or deleting residues. There are also tools to enter a new sequence, generate an MSF, or change the hydrogen representation of the molecule.
The protein modeling tools are divided into two utilities: Model Backbone for defining main chain conformations, and Model Side Chains for defining sidechain conformations. They are closely interdependent. This utility includes tools to search the structure database for fragments to use in model building and a regularization and energy minimization tool.
This utility contains tools for modeling the protein side chain conformations. It is assumed that the protein main chain has been determined using the Model Backbone utility. This utility includes rotamer libraries and regularization and energy minimization.
This module provides tools that search a database for structures with similar folds to one active molecule. The search motif can be entire proteins or selected substructures.
This utility is concerned with sequence analysis. It can be used for sequences for which the structure coordinates are not defined. There are five different types of analysis that can be displayed, three of which are prediction methods. The results of the analysis are usually presented as plots of property vs. sequence position.
This utility follows the method of Bowie, Luthy, and Eisenberg. 3D protein structures are analyzed into 1D profile sequences. This method is used to generate a plot of the quality of a model.
This utility retrieves textual information on PDB files from the protein structure database by accessing the QUANTA file $HYD_LIB/database.dat. This database file contains information on all the PDB files currently in the Brookhaven Protein Databank. It is also the same data file used by the structural database utility.
This utility provides a group of options to search the Protein Data Bank for sequences that closely match a specific sequence. QUANTA uses the FASTA sequence search algorithm.
Searching the structural database aids in molecular modeling. Using this utility, a search can be performed on a specified sequence or conformation against all of the known protein structures from the Brookhaven Protein Databank. This information is found in the file $HYD_LIB/database.dat.
This utility superposes structures on the basis of their overall folding rather than requiring identifying homologous residues. Using this utility, protein structures with similar folding motifs, but possibly little other obvious homology, can be superposed.
The Protein MODELER application provides an interface to the automated homology modelling program MODELER. The application includes the Align and Superpose utility identical to that in Protein Design and tools to run and read MODELER results. There are tools for display and analysis of MODELER results.