ProteinShop 4.0

ProteinShop is an interactive tool for manipulating protein structures. It was designed to quickly create a set of protein configurations using human knowledge and intuition. These configurations can be subjected to local or global optimization. Although ProteinShop
does not perform the global optimization process itself, it provides a
framework that can be used to interact with a global optimization process
that may be running on a remote machine.

ProteinShop presents three levels of functionality

Level I: Display a 3D protein structure

· Create a 3D protein "from scratch", i.e., one amino acid at a time, from an amino acid sequence and secondary structure predictions.
· Load a 3D protein structure from a PDB file.
· Provide standard visualization techniques such as atom sphere, bond stick, and cartoon rendering.

Level II: Interactive manipulation of the 3D protein structure by changing dihedral angles along its backbone

· Manual secondary structure alignment by dragging selected secondary structures (alpha-helices and beta-strands).
· Change the shape of beta-strands by allowing twisting, curling, and pleating.
· Form parallel/antiparallel beta-sheets automatically.
· Save/load fragments of the protein for reuse in other configurations.
· Help align secondary structures to form tertiary structures by providing visualization guides and markers such as hydrogen bond rendering and atom collision visualization.
· Change secondary structure types for selected amino acids "on-the-fly" to experiment with weak or conflicting secondary structure predictions.
· Evaluate the energy of a 3D protein structure using externally provided energy computation code.
· Visualize calculated energy.

Level III: Monitor/steer a (remote) global optimization process

· Connect to / disconnect from a global optimization process.
· Download candidate configurations from an optimization process.
· Upload manipulated configurations to optimization process.
· Monitor optimization process by downloading entire tree of configurations.

Here are some key features of "ProteinShop":

· It helps researchers automatically generate tertiary structures from sequence and secondary structure predictions available from prediction servers accessible via the Internet.
· It enables scientists to apply their biochemical knowledge and intuition during interactive manipulation of protein structures.
· It provides visualization of free energy computed during modeling to facilitate comparison and analysis of alternative structures.
· It accelerates the discovery of low-energy configurations by applying local optimizations to user-selected protein structures.
· It automatically creates a variety of beta configurations based on probabilities for beta sheet topologies and matching alignments.

Requirements:

· OpenGL or GL for 3-D rendering
· FLTK for GUI
· AMBER for energy computation

INSTALLATION:

Use standard Makefiles included in the src directory.
Go to the "src' directory then type 'make' to build ProteinShop.

*** FLTK setting in the Makefile
The compiler expects include files under $(FLTK_BASE)/$(INCDIR), libraries under $(FLTK_BASE)/$(LIBDIR), and any needed build tools under (FLTK_BASE)/$(BINDIR). If you have a different setup, you need to hand-edit the compiler flags below.

FLTK_BASE = /usr/local

On some installations, Fltk OpenGL functions are in a separate
library, libfltk_gl. If the linker complains about undefined
symbols, try adding -lfltk_gl to the line below before -lfltk.

FLTK_LIBS = -L$(FLTK_BASE)/$(LIBDIR) -lfltk_gl -lfltk

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