MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions
The MolADI website provides a simple and clear service for
protein-small molecule dynamic visualization. The original
intention of the entire website is to enable users to
analyze and obtain results more easily. Users only need to
upload the data files they want to analyze, and can obtain
the results quickly. After testing, the analysis time is
about 30s, which is more efficient than manual analysis.
The results page also provides a wealth of visual results,
including 2D and 3D results. The information of each
interaction between protein and small molecule can be
clearly viewed, such as the location where the interaction
occurs, the distance and angle of the interaction, and the
interaction in the entire track changes, etc. At the same
time, MolADI's multiple filter functions also allow users
to locate different interactions of small molecules more
easily to further analyze their specific information in
the binding site of the receptor, such as how the distance
and angle change in the dynamic trajectory.
Quick Start:
Input:
Figure shows the homepage of MolADI, where users can upload files.
Users should provide a structure file in pdb format and a trajectory
file in xtc or gro format from GROMACS. The server will automatically
process different file formats in the background and proceed to the
next step. After jumping to the analysis interface, the front-end page will
display some current analysis progress information in real time. The average
time for analyzing one file is about 30s.
Overview Page
Figure shows the overview of the result page. The page is divided into
two areas. The left half is the 2D interaction information map, which
is displayed in the form of a radar chart. The right half is the 3D
interaction information. The function column contains the corresponding
residue information, the atom pair in interaction and their distance.
The area in the page can be zoomed and moved to adjust the viewing angle.
The initial result contains all the interaction information related to small
molecule in the data file. In the function column on the right, users can
select the interaction information of interest to observe. The functionalities
are listed below:
♥ Custom displaying information about the type of interaction of interest
There are in total of nine selection boxes in this functional area, including eight
specific interaction types, as well as whether to display all of the interactions.
The user can click on the selection box of the corresponding type to decide whether
to display the corresponding interaction type. The color corresponding to the
interaction type is also marked in this area, so that users can better understand the results.
♥ Custom selecting small molecules
This function is used to select which interaction information of small molecule
will be displayed. All interactions are displayed by default. All the small molecules
are listed in the list. By selecting the interaction of a specific small molecule of
interest to display, the contents of two regions (2D region and 3D region) will
correspondingly change to show the information of the selected small molecule.
♥ Whether to display the interaction information only
This function is for users to easily observe the interaction information. By default,
the structure diagram will be displayed to the user. However, if there is a lot of
interaction information generated and the structure is more complex, the structure
information may cover the interaction information. This function can be selected
to display only the interaction information to better observe the corresponding
interaction information.
♥ Camera type
This function provides a stereoscopic display effect, the user first needs to
select the stereop mode, and then wear professional glasses to observe the stereoscopic effect.
♥ Center
This function is used to locate the 3D result to the center of the page to facilitate
the observation the result.
The above functional areas can be used freely and flexibly to meet the needs for
different observation requirements. Finally, the result download function is provided
in the upper right corner of the overview page, and the result is saved as a pdf file
for users to download. It mainly includes 2D result information.
3D Result Page
Figure shows the function of the 3D page, which is mainly used to display
3D results, providing a larger area for users to better observe the results.
Compared to the overview page, a dynamic result display has been added to
this page: by clicking the play button in the functional area, the 3D result
will play the trajectory and show the interaction information from each
frame in a dynamic and circular sequence. The movie can be paused to locate
the frame of interest. More conveniently, by sliding the scroll axis on the
right side of the button, the user can directly locate a frame to observe.
Similarly, this function can also be used in conjunction with other functions
of the functional area. For example, users can choose to only observe the
dynamic changes of hydrogen bonds of specific small molecules.
2D Result Page
Figure shows the 2D result page, which mainly reflects the interaction
information through 2D graphs. In the left half of the area, all
interactions are listed in table form. On the right, the first row
is the radar chart on the overview page. Note that the list and the
radar chart are in one-to-one correspondence. The corresponding interaction
can also be selected and displayed through the small molecule selection
function (top left). The second row on the right is the heat map of
interaction, which reflects the dynamic interaction information in the
2D form, and shows the interaction variations along the trajectory used
(when there are less than 50 frames, only the corresponding frame has its
interaction information ). The X axis shows the frame serial number.
In this figure, a total of 50 frames are selected from the trajectory
file uploaded by the user at an intermediate interval. The Y axis shows
the specific interaction information, including the interaction type,
residues and/or the small molecules involved and the small molecule id.
From the heat map, users can clearly see the dynamic changes of a
specific interaction in the entire trajectory. The bottom row reflects
the stability of the protein structure in the trajectory.
The backbone-backbone RMSD, backbone-backbone RMSF, and backbone-ligand
RMSD are shown