Protein Chain: the user
can enter a PDB code or upload his/her own PDB format file. If
the input structure includes more than one chain, the user will be requested
to select one of the chains in the next step. The server employs coarse
grained residue model and thus only reads
Ca atom coordinates from the PDB file, so the input file may include
only Ca atoms. Missing residues in
the input PDB file, are neglected in the calculations and the results are
oriented according to available parts.
E-mail address (optional):
since the calculations may take up to a few minutes for long proteins, it is
recommended to enter e-mail address as an input. Once the calculations are
finished, the link to the results will be sent to this e-mail. The results
will be kept in the server for 2 months.The results page, if bookmarked, can
be reached during this period.
Currently HingeProt focuses on single chain of a
protein. The largest number of residues allowed is 999. For a more detailed
help on the theoretical background of the work
see the About page.
Results are given for the first and second slowest GNM
modes of motion and their corresponding ANM modes of motion.
The server provides a table in which the rigid
parts and the hinge residues calculated using the slowest first and second
modes are given. Hinges dividing rigid segments and short flexible
fragments on the rigid segments are displayed as a separate list after rigid
parts. The two predicted conformations that describe the fluctuations from
the average structure in the slowest first and second modes are presented
and also available for download.
For each mode, the server provides a PDB format coordinate file.
An arbitrary temperature factor is assigned to each rigid part so that when
colored by temperature factor, each rigid part is shown in different color.
The output files contain three models of the protein chain. The first model
is the original chain (x-ray or NMR structure or a model structure), the
second and the third models are predicted chain conformations obtained by
adding the fluctuation vectors (+/-) in the respective modes to the
equilibrium position vectors (average structure).
Jmol script is provided to view the results online. However the output
files may be downloaded for later use. For visualization, any software that
is capable of opening different models at the same time and coloring
residues according to temperature factors is appropriate. Rasmol is suitable
for the specific purpose.
Below is given an example output of HingeProt. Each
section may be summarized as follows
name of the pdb and chain user selected is displayed here.
:When the script first
loads, original pdb of the structure is displayed in the window. User
then may observe the rigid parts in different colors and the
fluctuations at each mode by pressing "Slow Mode 1" and "Slow Mode 2"
buttons. User may also display the residue numbers by pressing right
mouse button on the window and choosing Labels/Atom number.
:The PDB file
displayed by Jmol representation may be
downloaded here. Each rigid body is assigned a different
(arbitrary) temperature factor so that when colored by temperature
factor, each rigid unit is displayed in different colors. +/-
fluctuations are given as separate models in PDB file. To be able
visualize the motion all models have to be loaded.
Rigid Part No
number of rigid part.
Numbers corresponding to each rigid part are given according to
original PDB index.
list of hinge residues separating rigid segments is displayed.
Short Flexible Fragments
segments with less than 15 residues are assigned to the nearest rigid
segment and displayed as "short flexible fragments" in this list.