1. Lab of Computational Biology Avatar Lab of Computational Biology
  2. Aggrescan3D
  3. Aggrescan3D

Wiki

Clone wiki

Aggrescan3D / Home

View History

Aggrescan3D logo

Welcome to Aggrescan3D wiki page! Installation instructions are provided on Agrescan3D OVERVIEW PAGE

Table of contents

1. Aggrescan3D outline

1.1 Automated mutation workflow

2. Aggrescan3D dependencies

2.1 General dependencies

2.2 Base program dependencies

2.3 Graphical interface dependencies

3. Aggrescan3D options

3.1 Input options

3.2 Output options

3.3 Mutation options

3.4 Dynamic mode options

3.5 Accessibility options

4. Aggrescan3D output

4.1 Base output

4.2 Optional output

5. Aggrescan3D graphical interface

5.1 Outline

5.2 Getting started

5.3 Important notes

5.4 Running a simulation

5.5 Managing your projects

5.6 Output analysis

1. Aggrescan3D outline

Aggrescan3D (A3D) is aimed to predict the aggregation propensities of proteins in their folded states. A3D uses as input protein 3D-structures, derived from X-ray diffraction, solution NMR or modeling approaches in pdb format. The structures are energetically minimized before their analysis. The method exploits an experimentally derived intrinsic aggregation propensity scale for natural amino acids and projects this scale in the protein 3D structure. In the A3D method the intrinsic aggregation propensity of each particular amino acid in the structure is modulated by its specific structural context. Aggregation propensity is calculated for spherical regions centred on every residue Cα carbon. This provides a unique structurally corrected aggregation value (A3D score) for each amino acid in the structure.

A3D discards the negligible contribution of highly hydrophobic residues hidden in the core of folded proteins to aggregation and focuses the prediction on protein surfaces. This structure-based approach identifies aggregation patches that are typically not contiguous in sequence like those identified by linear sequence or composition-based algorithms, outperforming them.

The identified aggregation prone residues or their surroundings can be virtually mutated to design variants with increased solubility. The selected mutation/mutations are modelled and a new A3D prediction is subsequently generated on top of this new structure.

The dynamic structural fluctuations that a protein experiments in solution influence its aggregation propensity, promoting partial exposure of usually buried residues. In this way, mutations leading to destabilized protein variants with increased conformational fluctuations usually have a huge impact on the aggregation propensity of the protein. For this reason A3D can be also run in Dynamic Mode. In this mode, A3D exploits the CABS-flex approach for the fast simulations of near-native dynamics of globular proteins. The aggregation properties of the ensemble of protein models are analysed and the most aggregation-prone conformer is selected as a proxy of the aggregation promoting state in the particular protein of interest.

Please note: Aggrescan3D was tested and developed with FoldX calculations preceding the analysis. The results which do not include this step should be analyzed with extra caution.

FoldX is free for academic users and can be acquired here

The program's simplified pipeline can be found below.

Aggrescan3D pipeline

1.1 Automated mutation workflow

This module automatically identifies the strongest APR's (aggregation prone regions) in the protein's structure and suggests a series of point mutations (into glutamic acid, arginine, lysine and aspartic acid) that would increase the protein solubility without impacting its stability. The workflow is as follows:

  • Optimize the input structure
  • Identify the APR's using the Aggrescan3D method
  • Mutate selected residues
  • Analyze the results for each point mutant

Aggrescan3D paper: AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures Nucleic Acids Research, 43:W306–W313, 2015

2. Aggrescan3D dependencies

2.1 General dependencies

  • Python 2.7 - The base program as well as the GUI is written in python 2 and some of the syntax requires the 2.7 version. This should be installed in most UNIX distributions by default.

  • pip and setuptools - Pip is a python package manager that is not needed for this project but is highly recommended for less experienced users, since it provides the fastest and easiest way to get Aggrescan3D running with all necessary packages. Installing pip should automatically install setuptools in most cases.

  • Python packages - Some packages needed for the program's functionality are not present in python default distributions. In most cases the process of installing those should be done automatically when installing the Aggrescan3D package. The base program requires setuptools and then it will take care of the dependencies for the user. For the GUI flask, and several other packages are needed to run the local server, the whole list can be found in the requirements.txt inside the a3d_gui folder. These will be installed for you via pip on the first run if they are not present.

2.2 Base program dependencies

Some functionalities of AGGRESCAN3D are based on external programs.
Here is a full list of programs and dependencies needed for specific options. Please note that currently only linux systems are supported.

  • Stability calculations - Each structure can undergo stability calculations for improved prediction if the user has the FoldX program installed. --foldx option has to be used.

  • Mutate - Requires FoldX program to be present on the system. In order to use the mutate option, --foldx * option must be used with its value pointing to the FoldX program location.

  • Automated mutations - Requires FoldX program to be present on the system. In order to use the mutate option, --foldx * option must be used with its value pointing to the FoldX program location.

  • Dynamic - requires CABS-flex standalone application to be present on the system. If CABS-flex is installed no further options are needed. If CABS-flex is installed but not present on the system, --cabs_dir with path to CABS-flex must be provided.

  • Movie - In order to generate a movie PyMol and avconv packages must be installed.

  • Naccess - csh shell is mandatory to run Naccess. Although freeSASA is the main accessibility calculating program, naccess is also supplied for cross-reference and because it was used in the tests and for the publications results. The csh shell should be available for all unix distributions in their respective repositories. For ubuntu do: 

    #!bash
sudo apt-get install csh
    For some systems the package might be called tcsh, for example: 
    #!bash
yum install tcsh

2.3 Graphical interface dependecies

Aside from the ones needed for the base program to work, the graphical interface might require some additional features to function properly:

  • Aggrescan3D base program - In order for the GUI to run simulations Aggrescan3D program must be installed (via provided setup.py script or otherwise).

  • Free port number 5000 - The server runs on port 5000 locally by default. If any other service is using the port or flask's socket it might not be possible to run the GUI. If this happens contact us for more assistance.

  • Working internet connection - It is advised to have an open internet connection at all times when using the GUI as some of its functionality is dependent on web based JavaScript libraries.

3. Aggrescan3D options

3.1 INPUT OPTIONS

3.2 OUTPUT OPTIONS

3.3 MUTATION OPTIONS

3.4 DYNAMIC MODE OPTIONS

3.5 ACCESIBILITY OPTIONS

-i, --protein <PDB>

Input structure. Aggrescan3D accepts either pdb codes (which are then downloaded from the pdb database, hence requiring an active internet connection and an open port) or a pdb file. The file should be in ABCD.pdb.gz or ABCD.pdb format.

Default value: None
Possible values: Path to PDB file, PDB code
Example: -i 2GB1

-C, --chain <CHAIN>

Only consider a specific protein chain while performing the simulation ignoring the rest of protein chains (if available). If not provided, all of the protein's chains are taken for the Aggrescan3D analysis.

Default value: None
Possible values: One letter that is a valid chain identifier for the selected protein
Example: -C A

-c, --config_file <CONFIG_FILE>

A config file that sets up the program's parameters. Please do note that command line options will override the config file. Detailed instructions on how to create a config file can be found in configReade.ini file downloaded with the package.

Default value: None
Possible values: Path to a config file
Example: -c configReadme.ini

-D,--distance <VALUE>

Distance cutoff used in calculations. This is the maximum distance in Angstroms from the central residue at which other residues will be considered in Aggrescan3D calculations.

Default value: 5
Possible values: 5, 10
Example: -D 10

-f,--foldx

The program will attempt to run foldX on the provided pdb file or code in order to optimize it before Aggrescan3D calculations are performed. If not provided the program will treat input pdb as if it was already optimized. This option is required for the mutation option to work.

Note: The path used (if valid) will be saved to a file and the option can then be used without arguments (just -f).

Default value: None
Possible values: Valid path to foldX program installed on the system
Example: -f /home/example_user/FoldX/

-v --verbose <VALUE>

This option changes the way Aggrescan3D logs it's progress.

  • 0 - Only critical messages will be displayed (usually this means that simulation failed or encountered a serious issue)
  • 1 - Warning messages will be displayed as well, these are usually minor issues or situations that might need user's attention
  • 2 - Info. This is the default behavior, messages about program progress will be displayed
  • 3 - Log files. This verbosity level will dispay messages concerning file managment
  • 4 - Debug. The program will report as much and accurately as it can about what it is doing. Exceptions will be raised to provide Python traceback, and all temporary files will be kept after the simulation is finished.

Example: -v 4

-r, --remote

Redirect the program's standard output and standard error to a Aggrescan.log file that will be created in the program's working directory rather than displaying the messages in the terminal. This option also turns off the log's coloring and if an Aggrescan.log file already exists in the selected working directory it will be appended to and not overwritten.
Please do note that attempting to pipe the output will not work in this case as it is internally redirected to the file.

Default value: None Example: --remote

-M, --movie <FORMAT>

A short movie of the protein is made with selected extension which can later be viewed using provided server-like interface or otherwise used.

Default value: None
Possible values: mp4, webm
Example: '-M webm'

Pymol and avconv packages are explicitly called to create the movie so both must be installed.

-m, --mutate <VALUE>

Provide a mutation or mutations that are to be applied to the input protein. Multiple mutations can be added with a single -m line and the -m option can be used multiple times (Be careful not to mutate a single residue multiple times, this will cause undefined behavior). The mutant is build using FoldX software, alternatively a mutant might be built outside the program and supplied as regular input.

The syntax for the option:

-m <Old residue><New residue><Residue index><chain ID>

Note: This option requires the --foldx option in order to work.

Default value: None
Possible values: Valid mutation(s) for the protein
Example: -m MW1A

-am, --auto_mutation <OPTIONS>

Automatically predict more soluble mutants. This will choose x residues and attempt 4 mutations on each (into glutamic acid, arginine, lysine and aspartic acid). Selecting a large x might result in a long simulation. The second argument is the number of cores used concurrently to perform the calculations. An optional argument to this option is a list of residues that will be "fixed" - not considered for mutations.

The syntax for the option:

-am '<maximum number of mutated residues> <number of cores used> [list of excluded residues in a form of <residue ID><chain ID>]'

Note: This option requires the --foldx option in order to work.

Note: We advise the number of used cores to be the number of physical cores of your PC or less.

Note : The parenthesis should be omitted in a config file.

Default value: False ('2 2' when the option is used without any arguments)
Possible values: Any number of resides and cores Example: -am '2 2 1A 2B 3C'

Alternative mutation syntax

{'idx': 'residue id', 'chain': 'chain id', 'oldres': 'old residue one letter code','newres': 'residue to insert'} Mutations can be specified in a config file where each line is matched against a specific pattern. One needs to specify: Residue ID, chain ID, old residue one-letter code and new residue one-letter code. The program expects a JSON-like formatted line. Please make sure each mutant is separated by a newline as otherwise parsing might fail.
Example lines:
{'idx': '1', 'chain': 'A', 'oldres': 'M', 'newres': 'W'}
{'idx': '2', 'chain': 'B', 'oldres': 'T', 'newres': 'P'}

-d, --dynamic

Use CABS-flex to simulate the protein flexibility and generate 12 models (by default) that are then evaluated for their Aggrescan3D score and then the most aggregation prone model is chosen as a basis for the final analysis. See the overview or the paper for more details.

Default value: None
Example: '-d'

To use this option CABS-flex application must be installed on the system. Download and see how it works

--n_models <VALUE>

Tell CABS-flex to create a custom number of models for the Aggrescan3D analysis. Please do note that this option doesn't make the simulation longer and the same number of intermediate models are created during simulation so selecting more models won't necessarily make for better results, only that more medoids will be selected. See CABS-flex wiki for more informations.

Default value: 12
Possible values: Any number (though a range of 5-25 would be recommended)
Example: --n_models 10

--cabs_dir <PATH>

Provide a specific directory from, which CABS-flex should be run rather than from a user or system-wide installation. This option is a convenience for users who might need it and should be negligible in most cases.

Default value: None
Possible values: Valid path to a CABS-flex folder (the one with code called "CABS", not the entire repository)
Example: --cabs_dir /home/user/path/to/CABS

--cabs_config <PATH>

Provide a path to a CABS config file which will be used by CABS to run the simulation. This gives the user almost full control over the simulation. This comes with a cost however as it is up to the user to supply a valid CABS config file as it will not be parsed by the Aggrescan3D program in any way. Should CABS simulation fail, a CABSerror file will be created in your working directory which should give more insight on what went wrong. See the CABS wiki to learn more.

Rules of creating CABS config files:

  • Do not use the --work-dir option as it might disturb the flow of Aggrescan3D execution
  • Do not use the --input option. It will get overwritten anyway
  • The --n_models aggrescan option will overwrite --clustering-medoids in the CABS config file (best not to mix the two)
  • --aa-rebuild and --remote options will be added to the config by default

Default value: None
Possible values: Valid path to a CABS-flex config file
Example: --cabs_config /home/user/path/to/config.ini

-n, --naccess

Both naccess and freeSasa are solvent-accessible surface area calculating programs that are used to determine the Aggrescan3D score. By default the program uses freeSasa but one can use naccess instead.

  • See the dependencies instructions for informations on troubleshooting this option.

Default value: None Possible values: naccess
Example: --naccess

4. Aggrescan3D output

4.1 Base output

Score table

By default Aggrescan3D will produce an A3D.csv file in the working directory with values separated by commas.

Where the columns go as follows: 1. Protein - an internal name used by the program 2. Chain - the one letter chain ID 3. Residue - residue's index 4. Residue_name - A one letter identifying the amino acid 5. Score - Aggrescan3D score

Score plots

For each of the chains in the protein two plots will be generated. One in svg and one in png format with names like chainID.png, for example: A.png.

Pdb files

Two pdb files should be present at the end of simulation: 1. input.pdb - the input file (a input.pdb.gz file might also be present if the structure was downloaded from the pdb server). 2. output.pdb - the result of the simulation with b factor field replaced with A3D score.

Config file

A config.ini file should be generated for each run. These are useful if one wishes to re-run the simulation with the same setting changing only some of them (command line options overwrite those specified in config, so aggrescan -c config.ini -w /other/dir will re-run the simulation with a different working directory).

This file is also needed for the GUI so that the project can be added to the database.

4.2 Optional output

Movie

  • When the -M flag is used a clip.webm or clip.mp4 file will be present in the working directory at the end of simulation.

Mutation

  • When a mutant is created a MutantEnergyDiff file is created which contains the energy effect of the mutation in kcal/mol calculated by FoldX.

Dynamic mode

In dynamic mode several new files are created:

  1. avergaes - Json like formatted file with Aggrescan3D score for each of the CABS-flex generated models.
  2. CABSflex_rmsf.csv - tab separated file with two columns: Residue ID (Chain letter + residue index, for example A13) and RMSF score calculated by CABS-flex.
  3. CABSflex_rmsf.png - a plot of the RMSF.
  4. CABSflex_supe.png - This file is only generated when PyMol is installed. A superposition of the input structure and the most aggregation prone model.
  5. models.tar.gz or model_x.pdb - All the models generated by CABS-flex. If the GUI is used the tar gz archive is extracted.
  6. stats.tar.gz or model_x.csv - Aggrescan3D analysis for each of CABS-flex models. The file is formatted similarly to A3D.csv. If the GUI is used the .tar.gz archive is extracted.

Automated mutations mode

In this mode several new files with mutation's analysis are created. The mutation code mentioned is in format of <Old residue> <New residue><Residue ID><Chain ID> (for example VM1A if the 1st residue of chain A - methionine is mutated into valine). The Short code refers to a single mutated residue and is in format of <Residue ID><Chain ID> so would be 1A for previous example.

  1. Mutations_summary.csv - CSV file containing the energetic and solubility effect for each created mutant
  2. <Mutation code>.csv - CSV file with A3D scores of each residue for the specific mutant
  3. <Mutation code>.pdb - PDB output file with the mutant's structure
  4. <Short code>.png - Plot of A3D score for each mutant of the specific residue with the wild type as a baseline (png format)
  5. <Short code>.svg - Plot of A3D score for each mutant of the specific residue with the wild type as a baseline (svg format)

Log file

  • When ran with --remote option an Aggrescan.log file will be created.

Error files

  • Whenever the program encounters an error that stops its execution an Aggrescan.error file will be created. If CABS-flex is the program that failed a CABSerror file will also be created. Inspect the contents of those files for more details on the errors.

5. Aggrescan3D graphical interface

5.1 Outline

Aggrescan3D's graphical interface is a server that is hosted and accessed locally on user's machine with no outside access to the server. This is done using flask framework. The goal is to provide a web-server like functionality but without all the limitations, that means an easy to use, lightweight interface that would allow users to run their simulations and more importantly see the data visualizations with a few mouse clicks.

The program is intended to be used on a single PC but with some technical prowess could easily be adjusted to be run on servers and clusters.

5.2 Getting started

To start the GUI issue a following command: 

#!bash
a3d_server

If it is your first run of the command you should be prompted for a path to your FoldX installation (if you don't have one simply click Enter). To perform stability calculations with the gui type in the absolute path like /home/user/FoldX. The path will be checked for you. The path can always be updated via the gui itself.

On the first run your system will be checked for the necessary Python packages. In the unlikely case that one of the packages could not be imported a pip install command will be issued after the user's consent. Issues with this step might indicate an issue with Python itself (for example double pip/conda package installations and such).

If pip is not installed on your system install it with 

#!bash
sudo apt-get install python-pip
sudo pip install --upgrade pip

Or go to pip's web page and follow the instructions there.

After the server has started open up your favorite web browser and go to 0.0.0.0:5000 or simply click on the "0.0.0.0:5000" text that should be displayed and underlined after starting the server.

Windows users most likely need to use localhost:5000 instead (also if the server is not responding after starting up it is advised to try that on other systems as well as the exact address will depend on host's machine loopback settings).

5.3 Important notes

  • Internet explorer will not provide full functionality of the app.

  • It is advised to keep the app running while calculations are performed. Closing the web browser will not stop the app. Closing the terminal it is ran from will.

  • For Windows users: in case of the app not loading or not responding to button clicks try issuing a single CTRL+c to the command line terminal you used to run it as some software might occasionally block it.

  • Most of the options in the GUI have help boxes displayed as small black dots. Mouse over them to see an explanaton of what the option does.

  • In this section one can find screenshots of the GUI and below them detailed explanations of each option.

  • Please do note that for the gui to function the server has to stay open in the terminal. It might produce a lot of messages which can be safely ignored.

  • Because the program is still in development the screenshots on this wiki might slightly differ from the program itself

5.4 Running a simulation

The following page, which is the main page serves also as a job running page. On the right panel one can find input panels which are explained below and the relations between the command line options and the GUI options are explained.

Your input is always validated before running a job. If something goes wrong error messages will be displayed on top of your screen.

Aggrescan3D Index_page

Input Structure

  • PDB code / Local PDB file - Equivalent to -i or --input.It is the only necessary input provided as a 4 letter code or as a local pdb file which can be chosen via the "Browse button".

  • Chain - Equivalent to -C or --chain. Enter a one letter, uppercase chain ID to select only that specific chain for the simulation.

Options

  • Project name - A name identifying the project that will appear in your Project manager tab. If not specified a random sequence of characters and numbers will be assigned to the project.

  • Stability calculations - Equivalent to -f or --foldx. If selected FoldX will be used for stability calculations before aggregation analysis is performed.

  • Dynamic mode - Equivalent to -d or --dynamic. If selected, CABS-flex will be run and a dynamic tab will appear in your results page where 12 CABS-flex generated models can be thoroughly analysed.

  • Mutate residues - Equivalent to -m or --mutate. If selected a new page will appear where mutations can be manually selected. Requires Stability calculations to also be selected.

  • Distance of aggregation analysis - Equivalent to -D or --distance. The distance of aggregation analysis around the central residue. See more

  • Enhance protein solubility - Equivalent to -am or --auto_mutation. Automatically enhance protein solubility by point mutations. Read more

FoldX settings

  • Change your FoldX path - enter a path to your FoldX installation so that Stability calculations can be performed.

5.5 Managing your projects

Project manager tab

By clicking on the project manager in the main navigation bar at the top of the page you enter the manager:

Aggrescan3D Project_manager_page

Add project panel

  • This panel allows to add a manually run project to the GUI's view and database which allows for analyzing its results using the interface.

  • Add a project - click on the "Choose file" button and navigate to your Aggrescan3D's project folder and select a config.ini file (those are generated automatically for each run).

  • Choose a project name - Optional, add a name that will help identify the project later on. If not provided a random sequence of characters and numbers will be assigned as the project's name.

  • Add project! - When everything else is done click on this button to add the project.

Your projects panel

  • A list of all of your projects recorded in the database.

  • Click on the project's name to go to it's detailed page.

  • The project status can take on the following values:

    Done - The project is done and its results can be explored

    Running - The simulation is running and one has to wait for it to finish

    Missing files - This status applies to any situation where there is no error but the project is missing files that would indicate it is completed. This can mean that some files were deleted or that the project is running but was ran manually and the GUI can't track its progress (But the user can see the log if the simulation was ran with --remote)

    Error - Aggrescan3D or any of its subprograms encountered an error. See the log for more details and if it is of no use contact us for further assistance.

Project details tab

This tab contains detailed information about your project. This page can take two forms. When the project is done:

Aggrescan3D Details_tab

When the simulation is running two additional buttons appear:

Aggrescan3D Details_tab

  • Stop the job - The project's status will be set to error and a signal stopping Aggrescan3D's process and its children will be sent leaving the simulation in the middle. This would be almost equivalent to hitting CTRL+c

  • Stop and delete the files - Aside from the above actions the entry for this project will be removed from the database and all the related files will be deleted.

Manage project tab

This is the main tab for manually managing the projects status.

Aggrescan3D Manage_tab

  • Change the job status manually - In most cases the program will try to deduct the status of your project by itself while its status is not final. This means that when the project is 'Running' and 'Missing_files' the program will attempt to check if it has finished or encountered an error. You can however find yourself in situations where you made changes to the files manually and now want to change the status yourself. Set it to "Running" if you wish for the program to deduct the status automatically.

  • Rerun this job - This button simply attempts to re-run this job with all the settings intact. This will naturally overwrite any results previously present in the working directory. Otherwise the only immediate effect is a reset of the Aggrescan.log file.

  • Delete this job - Remove either only the database entry or any reachable files associated with this project. If the project is not run from within the GUI it might reside in a folder containing important data, please be careful when using this option. While theoretically this shouldn't happen this action might lead to a data loss inside the project's working directory.

5.6 Output analysis

Aggrescan3D's GUI offers several ways of visualizing your data once the simulation is over.

Plot tab

An interactive plot showing Aggrescan3D score for each residue. Aggrescan3D Profile_tab

  • Show chain - Use the drop down menu to choose a chain to display
  • Show buried residues - Show residues that have a score very close to 0. Those residues do not contribute to the aggregation and are hidden by default.
  • Mouse over a plot entry to see details of the data point (as shown on the screenshot)

Score tab

An interactive table of Aggrescan3D score, score statistics for the whole protein and an option to re-run the job with new mutations. Aggrescan3D Score_tab

  • Show chain - Use the drop down menu to limit the table to a specific chain
  • Show residues from : to - Select a range of residue indexes to display. If no chains are specified the selection applies to all relevant chains.
  • mutate - When clicked a small window will appear where a mutation for the specific residue can be chosen for a new job to be run.
  • Submit - Re-run the job with the same options but with new mutations. This button becomes active when at least one mutation is selected.
  • The table can be sorted in regard to any of the columns using small arrow-like buttons in the first row.

Structure tab

Protein visualization. Aggrescan3D Score_tab

  • Each residue is colored according to their A3D score.

    Blue - soluble (the darker, lover the score)

    White - buried (score ~0)

    Red - aggregation prone (the stronger the higher the score)

  • View in 3Dmol - Selected by default. Switch to an interactive display of the protein. One can zoom in and out or spin the model around for better view.

  • Stop/Start animation - Starts or stops the animation if 3Dmol view is active
  • Take snapshot - Create a picture from the current interactive view. The name of the file can be entered in the box above (note - duplicate names will get renamed)
  • Label residue - Enter a residue code, or a list of residue codes (<Residue ID><Chain ID>), for example "12A, 13B" to show labels on said residues
  • Show labels - Show labels for the aggregation prone residues (only in 3Dmol view).
  • Delete label(s) - Open a list of currently displayed labels, click on the chosen ones to delete them
  • Play the video - If PyMol is installed and the simulation was ran with -M or via GUI (-M by default) a short video of the protein will be played.

Dynamic mode details tab

There are three distinct parts of the Dynamic tab where each of the models generated by CABS-flex can be analyzed.

Model viewer

Aggrescan3D Dynamic_tab_1

  • View in 3Dmol - Each of the models can be selected and displayed. The viewer works exactly like the one in the Structure tab.

Score profile

Aggrescan3D Dynamic_tab_2

  • Plots offer several tools located at the bottom of the plot inlcluding: padding, zooming, resetting the plot and saving it as a file.
  • Mouse over the plot to see the details of each residue.

CABS-flex output - RMSF of the models and an alignment of the top model with the input structure

Aggrescan3D Dynamic_tab_3

  • The alignment is only available when PyMol is installed.

Automated mutation tab

There are two distinct parts of the Automated mutations tab where each of the mutants can be analyzed.

Model viewer

Aggrescan3D Dynamic_tab_1

  • View in 3Dmol - Each of the mutants can be selected and displayed. The viewer works exactly like the one in the Structure tab.

Score profile

Aggrescan3D Dynamic_tab_2

  • Click on the legend to show/hide selected mutant
  • Plots offer several tools located at the bottom of the plot inlcluding: padding, zooming, resetting the plot and saving it as a file.
  • Mouse over the plot to see the details of each residue.

This tab contains all the screenshots taken in this project.

Aggrescan3D Gallery_tab

Updated