Frequently Asked Questions
How does the CABS-flex method
work?
How to run flexibility
modeling?
How to use flexibility mode?
How to use advanced
simulation
options in flexibility modeling?
How to use and interpret
CABS-flex temperature?
How to use Residue-level
flexibility
control?
How to run peptide
modeling?
How to analyse
flexibility
modeling?
How to analyse peptide
modeling?
What are protein
restraints?
How to cite CABS-flex 3.0
server?
How to report issues with
CABS-flex 3.0 server?
How does the CABS-flex method work?
The CABS-flex 3.0 web server is designed to operate in two distinct modes: Flexibility Modeling and
Peptide Modeling, see pipeline below.

Flexibility modeling uses multiscale modeling pipeline merging CABS coarse-grained model with
all-atom reconstruction, see [CABS-flex 3.0 paper in review and
Protein
Sci 2024]. Peptide
modeling
uses modeling protocol described in [
Brief in Bioinfo
2024].
How to run flexibility modeling?
To begin a flexibility modeling simulation, you need to provide a protein structure in PDB format.
You can do this in two ways:
-
Enter a PDB ID – If your structure is available in the Protein Data Bank
(PDB), enter its four-character code in the "PDB code/PDB file" box.
-
Upload a PDB file – If you have the file on your computer, click “Browse”
to locate and upload it.
The
only required input is the protein structure. Other optional but important
settings include:
-
Flexibility mode – Pay attention to this setting, as it determines the
extent of structural fluctuations in the simulation. The default option is
Rigid, but you
can change it as needed. More details: [How to use
flexibility mode?]
-
Residue-level flexibility control – Modify flexibility for specific protein
fragments. See: [How to modify
residue-level flexibility?]
-
Project name – Helps identify your job. If left blank, a random hashcode is
assigned.
-
Chain selection – Choose specific chains from the uploaded PDB file.
-
Email notification – Get an email when the job is completed.
-
Privacy option – Enable “Do not show my job on the results page” to keep it
private (accessible via a direct link only).
The following screenshot shows the main page along with the discussed input options.

For additional customization, see: [
How
to use advanced simulation options?]
Once all parameters are set, click
"Run" to start your simulation.
How to use flexibility mode?
CABS-flex 3.0 introduces flexibility modes, which allow users to control how much different parts of
the protein can move. These modes define the range of residue movements by applying different
distance restraint schemes:
-
Flexible mode applies distance restraints only to residues forming secondary structure
elements, allowing greater flexibility in loops and unstructured regions. Previously
referred to as ‘SS2’ in earlier versions of CABS-flex 2.0 [Nucleic
Acids Res 2018] and standalone application
[Bioinformatics
2019], it provides a balanced representation of protein dynamics. This mode has been
validated
against crystallographic B-factors and atomistic MD simulations using various force fields
[J Chem Theory Comput
2013], NMR ensembles [Bioinformatics 2014], as well as in numerous structure–flexibility-function studies
supported by experimental evidence, including Cryo-EM–derived conformational variability and
functional analyses related to aggregation propensity and S-nitrosylation sensitivity [Protein Sci. 2024].
Importantly, the ability of the CABS model to predict loop structures ab initio has been
demonstrated across various protein systems [BMC Struct. Biol. 2010, Biophys. J. 2014], including in the context of peptide
interactions [Methods 2016], highlighting its suitability for modeling local structural variability.
-
Rigid mode imposes uniform restraints on all residues, minimizing fluctuations throughout
the structure. Equivalent to the ‘All’ mode described previously ([Nucleic
Acids Res 2018, Bioinformatics
2019], it effectively
preserves native-like conformational constraints. Benchmarking with CHARMM36m-based ATLAS MD
simulations showed high correlation with MD-derived fluctuation profiles, particularly in
structured, globular proteins [Comput
Struct Biotechnol J 2024]. It is worth noting that the selection criteria of the
ATLAS dataset favor well-folded, high-resolution monomeric proteins, which may bias the
dataset toward more structurally stable and less flexible systems. However, some degree of
intrinsic flexibility is still likely present in the selected structures.
-
Rigid-pLDDT mode improves flexibility predictions by integrating structural confidence into
the simulation process. In this mode, restraint strength is modulated according to
per-residue pLDDT scores and secondary structure classification, as introduced in our recent
work [Comput Struct
Biotechnol J 2024]. It is applicable when pLDDT scores are available, as in
AlphaFold-predicted
structures. Users may supply pLDDT values either through the B-factor field in the PDB file
or via an external .json or .tsv file. Based on general observations, the overall level of
flexibility generated by this mode tends to be closer to Rigid than Flexible, which is
reflected in the naming convention, and the mode has been validated using ATLAS MD
simulation data [Comput
Struct Biotechnol J 2024].
-
Unleashed mode applies no restraints, allowing for fully unrestricted conformational
sampling. The resulting ensemble is governed solely by the intrinsic properties of the CABS
coarse-grained force field. This mode is designed as an advanced option, recommended
primarily for exploratory simulations where it is important to observe the behavior of a
system in the complete absence of restraints. While this mode typically shows lower
agreement with MD-derived fluctuation profiles and may produce exaggerated motions, it is
valuable for modeling folding/unfolding processes or large-scale transitions in disordered
or flexible systems. In such cases, meaningful results may require careful tuning of
additional simulation parameters, such as temperature and number of cycles. The
applicability of CABS-based simulations to disordered and unfolded protein systems has been
reviewed in our previous work [Int. J. Mol.
Sci. 2019], which discusses several case studies involving
disordered binding partners and unstructured regions.
By default, Flexible mode is enabled in CABS-flex 3.0 due to its versatility and proven
accuracy. For stable, well-folded proteins, the Rigid mode may be most appropriate. When pLDDT
scores are available, we recommend using Rigid-pLDDT, which incorporates structural confidence into
simulations and improves predictive accuracy. Conversely, for systems expected to undergo
large-scale motions or unfolding, the Unleashed mode can be used, with caution and additional
parameter tuning. When in doubt, we recommend running simulations with multiple flexibility modes,
particularly Rigid, Flexible, and Rigid-pLDDT, and comparing the resulting fluctuation profiles with
available structural or functional knowledge about the protein. This comparative approach can help
identify the most appropriate mode for a given system.
Examples of using each individual mode are illustrated in the Gallery.
CABS-flex 3.0 also offers a residue-level flexibility editor that allows users to manually assign
flexibility categories prior to simulation. This option is further described in section:
How to modify residue-level
flexibility?
The image below illustrates an example effect of distance restraint modes on backbone fluctuations
in the simulation. It shows, from the top left, the starting protein structure (PDB ID: 2f60 chain
K) colored by pLDDT, followed by output structures generated using different restraint modes: Rigid,
Rigid-pLDDT, Flexible, and Unleashed. Further details on these restraints were recently discussed in
[
Comput Struct Biotechnol J
2024].
How to use advanced simulation options in flexibility modeling?
Advanced options allow users to modify default settings based on their needs and available
information about the modeled system.

The options can be split into three distinct section, which are:
Flexibility Restraint Settings
These options refer mostly to automatically generated restraints (
What
are protein restraints?)
according to the scheme defined by the Flexibility Mode (
How
to use flexibility mode?).
Gap sets the minimum distance along the protein sequence for two residues to be bound with a
restraint. By default, Gap is equal to 3, which means for example that residue number 15 cannot be
restrained with residues numbered from 12th to 18th.
Minimum and Maximum set the allowed restraint length in Angstroms. The restraints will be
automatically generated only if the two residues are within these distances. By default Minimum is
3.8 Å and Maximum is 11.5 Å.
Keep restraints allows reducing the number of automatically generated restraints indicating the
percentage of restraints to keep. This option can be used in order to increase flexibility. The
number must be between 100 and 0. Restraints are randomly removed so that the final number of
restraints
Nfinal =
Nall
×
(
PERCENTAGE ÷ 100).
Finally, there are four fields related to restraint weights: CA restraints and side chain
restraints. In the CABS model, these restraints add to the total simulation energy when the distance
between restrained residues goes beyond a set limit. The higher the restraint weight, the greater
the energy penalty. There are two types of weights: Minimum weight, applied when the distance is too
small, and Maximum weight, applied when the distance is too large. The weights value must be
non-negative, but value equal to 0 makes the restraints non-existent.
Custom Restraints
Besides the automatically generated restraints, the users can input their own restraints imposed on
the modeled protein structure. The top panel is for the Cα–Cα restraints and the bottom panel is for
the side chain–side chain restraints (SC–SC). Restraints can be added either through the text box or
from an uploaded text file. The restraints are defined by the following syntax:
“
residue1id residue2id distance weight”, for
example:
“123:A 73:B 12.5 1.0”.
This example defines a single restraint between the 123th residue of chain A and the 73rd residue of
chain B to be at a distance of 12.5 Å with a restraint weight of 1.0.
Simulation Settings
This panel enables modification of the parameters that control the simulation.
Number of cycles (Ncycle) sets the total number of models saved in the trajectory to be equal to 20
x Ncycle. For example, setting Ncycle = 50 results in 20 × 50 = 1000 models in the trajectory.
Cycles between trajectory frames (Nskipped), sets the number of models skipped on saving models. For
example, when Nskipped = 100 every hundredth model will be saved. This field also indirectly sets
the total number of models generated, i.e. for Ncycle = 50 and Nskipped = 100, the total number of
generated models equals 20 × 50 × 100 = 100,000. However only 1000 of them will be written to the
trajectory.
Temperature of simulation (T) is a dimensionless value that controls how much movement occurs in the
system. Read more about the temperature in the section below:
How
to use and interpret CABS-flex temperature?
Seed for random number generation initializes the random number generator. This can be used to
ensure reproducibility of the simulation. If the same seed is used, the same trajectory will be
generated.
Disable centrosymmetric potential turns off the centrosymmetric potential in the CABS model, which
pulls residues toward the center of the modeled protein. This can be useful for modeling large
complexes or proteins with a high degree of disorder.
How to use and interpret CABS-flex temperature?
In CABS-flex, the temperature setting controls how flexible the simulated structure is. You can
think of it as a slider for structural mobility: the higher the temperature, the more the protein
can move during the simulation.
Although it's called "temperature", this value is not expressed in Kelvins and does not correspond
directly to physical temperature. Instead, it is a dimensionless parameter used in the underlying
Monte Carlo simulation algorithm to control the balance between structural stability and
flexibility. The value affects how easily the model explores alternative conformations—higher
temperatures allow for broader movement and more energetic transitions, while lower temperatures
keep the structure closer to the starting model.
A common question from users is: “How can I convert the CABS-flex temperature to Kelvins?”
The answer is: you can’t—CABS-flex uses reduced temperature, a concept from statistical physics,
which has no direct conversion to physical units. It simply scales how much conformational space the
model explores.
The default temperature is T = 1.4, which works well for most typical applications, offering a
balance between realistic fluctuations and overall structural integrity. If you're studying subtle
flexibility or near-native dynamics, this default is usually appropriate. For more extensive
motions—such as protein unfolding, large conformational changes, or modeling intrinsically
disordered regions (IDPs)—you can try increasing the temperature to values like 1.6 or 2.0.
This behavior reflects how temperature is used in the underlying CABS coarse-grained model, where it
plays a central role in balancing energetic preferences and conformational entropy.
The figure below shows how different temperature values affect the flexibility of protein G, a small
globular protein (PDB ID: 2gb1), simulated using the Unleashed mode. In this mode, no distance
restraints are applied, so the conformational sampling is driven solely by the internal force field
of the CABS model. As illustrated, higher temperatures lead to global fluctuations in the range of
approximately 8–15 Å, demonstrating the impact of temperature on conformational mobility.
How to use Residue-level flexibility control?
After selecting the
Residue-level flexibility control checkbox during job
submission, you are redirected to a dedicated page where you can manually adjust the flexibility
level for each amino acid.

On this page, a table displays every residue from the sequence with the following details:
- Residue ID
- Chain ID
- Residue Name
- Secondary Structure
- Distance Restraint Category
Both the secondary structure and the restraint categories are color-coded, with legends at the top
of the page explaining the color schemes. Each residue is initially assigned a distance restraint
category:
- 3: Strong rigidity and tight structural bonds to the input
- 2: Weaker restraints
- 1: Intermediate flexibility
- 0: Full flexibility
To
modify the category you can click on the category for the desired residue and
select a new category from the dropdown.

To
modify multiple categories at once click one of the buttons labeled
"category 0",
"category 1",
"category 2", or
"category 3". Then, click on multiple residues to update their category
simultaneously. To exit this multi-select mode, simply click outside the table or press the Esc key.

Once you are satisfied with your changes, click
"save changes and submit" to
proceed with your job.
How to run peptide modeling?
To start a peptide modeling simulation, you need to provide a peptide sequence in the "Sequence"
text box.
Once you've entered the sequence, click the “Run” button to submit your job.

Additionally, you can provide secondary structure information in HEC format (H = helix, E =
beta-strand, C = coil) by entering it alongside the sequence, separated by a colon. For example:
ALALA:CHHHH. If no secondary structure is provided, it will be predicted automatically using
NetSurf-P 3.0 [
https://services.healthtech.dtu.dk/services/NetSurfP-3.0/].
If you want to model cyclic peptides, you can do this in two ways:
-
Add disulfide bonds enables adding disulfide bonds between selected cysteine residues. Pairs
of cysteines, numbered according to the input sequence, can be specified and bonded by
clicking the "+" button.
-
Model cyclic backbone allows closing the backbone of the modeled peptide into a cyclic
structure.
Peptide modeling uses methodology described in [
Brief
in Bioinfo 2024].
The other options are mostly used to help with handling jobs. All these inputs are optional and they
include:
-
Project name, which can help you find your job in the queue list. If not provided, the name
will be replaced with a random hashcode.
Chain(s), can be used if you want to select only specific chain(s) from the uploaded PDB
file.
-
Email address, which will be used by the server to send an email notification about job
completion.
-
Do not show my job on the results page will hide the job from the results page. You can
still access the results via the direct link provided after submission.
How to analyse flexibility modeling?
When you initiate a new job in CABSflex 3.0, the interface starts with a single
Project
Information tab. This tab is split into two sections: the upper section shows basic project
details along with buttons to download the
input structure and output files, while the lower section provides in-depth details such as
rigidity, restraints, and simulation parameters.

After job completion, the page expands to include three additional tabs –
Models,
Contact Maps, and
Fluctuation Plot – each designed to help you
explore different aspects of the flexibility modeling results.
Models section leverages the interactive mol* viewer for 3D visualization and is
organized into three sub-tabs:
-
Structure:
Loads by default to display the starting conformation. It offers a “Flexibility coloring:”
dropdown (with options such as RMSF, pLDDT, and B-factor) and a “Structural coloring:”
dropdown (allowing you to color the model by sequence, chain, secondary structure, or choose
a custom monochrome color via a color picker).
-
Models:
Displays each of the 10 output models one at a time with next/previous navigation. It also
supports the same “Structural coloring:” options.
-
All models:
Presents all 10 models simultaneously in a secondary structure representation.
Across these sub-tabs, you’ll find buttons to download a tar.gz archive of all output structures,
toggle the display of the initial structure (aligned with the current model), show disulfide
bridges, reset the view, and—within the Models sub-tab—animate the model sequence in a carousel-like
loop.

Located on the right side of the viewer, these options allow further customization, including
full-screen mode and exporting high-resolution images.
Contact Maps section features an interactive Plotly map that lets you examine the
interaction interfaces between residues (both inter- and intra-residue contacts). Buttons above the
map let you choose the desired contact map, and clicking any contact zooms in on and highlights the
corresponding amino acids in the mol* viewer. The map displays residue numbers and contact frequency
values on hover, supports zooming, dragging, and can be downloaded as a PNG. Below the map,
additional buttons allow you to download a tar.gz archive with the contact map data and to display
disulfide bonds.
Fluctuation Plot Tab. Here you can explore an interactive 2D Plotly plot that
charts RMSF versus residue for a selected chain (choosable via a dropdown). The plot is flanked by
color-coded secondary structure representations that provide residue and structure details on hover.
If available, an option to view a pLDDT plot versus residue is also provided. A CSV download button
below the plot allows you to export the RMSF data.
How to analyse peptide modeling?
When you initiate a new job in CABSflex 3.0, the interface starts with a single
Project
Information tab. This tab is split into two sections: the upper section shows basic project
details along with buttons to download the output files, while the lower section provides in-depth
details and simulation parameters.

After job completion, the page expands to include three additional tabs –
Models,
Contact Maps, and
Fluctuation Plot – each designed to help you
explore different aspects of the peptide modeling results.
Models section leverages the interactive mol* viewer for 3D visualization and is
organized into two sub-tabs:
-
Models:
Loads by default to display each of the 10 output models one at a time with next/previous
navigation. It offers a “Structural coloring:”
dropdown (allowing you to color the model by sequence, chain, secondary structure, or choose
a custom monochrome color via a color picker).
-
All models:
Presents all 10 models simultaneously in a secondary structure representation.
Across these sub-tabs, you’ll find buttons to download a tar.gz archive of all output structures,
show disulfide
bridges, reset the view, and—within the Models sub-tab—animate the model sequence in a carousel-like
loop.

Located on the right side of the viewer, these options allow further customization, including
full-screen mode and exporting high-resolution images.
Contact Maps section features an interactive Plotly map that lets you examine the
interaction interfaces peptide residues. Clicking any contact zooms in on and highlights the
corresponding amino acids in the mol* viewer. The map displays residue numbers and contact frequency
values on hover, supports zooming, dragging, and can be downloaded as a PNG. Below the map,
additional buttons allow you to download a tar.gz archive with the contact map data and to display
disulfide bonds.
Fluctuation Plot Tab. Here you can explore an interactive 2D Plotly plot that
charts RMSF versus residue. The plot is flanked by
color-coded secondary structure representations that provide residue and structure details on hover.
A CSV download button
below the plot allows you to export the RMSF data.
What are protein restraints?
Protein restraints are artificial "forces" that keep pairs of residues at specific distances during
a simulation. They help control how a protein moves by limiting certain structural changes. The
restraints add to the total simulation energy when the distance between restrained residues goes
beyond a set limit. During the simulation, if the protein moves in a way that breaks a restraint,
the system applies a penalty to push it back within the defined limits.
Before the CABS-flex simulation starts, the server automatically generates distance restraints based
on the initial shape of the input structure and the selected Flexibility Mode
(
How to use flexibility mode?).
Users can also add or modify these restraints as needed
(
How
to use advanced simulation options?).
The restraint is defined by the following syntax:
"
residue1id residue2id distance weight”, for
example:
“123:A 73:B 12.5 1.0”.
This example defines a single restraint between the 123th residue of chain A and the 73rd residue of
chain B to be at a distance of 12.5 Å with a restraint weight of 1.0. The higher the restraint
weight, the greater the energy penalty.
How to cite CABS-flex 3.0 server?
When you use CABS-flex 3.0, cite the paper:
-
CABS-flex 3.0: An Online Tool for Simulating Protein Structural Flexibility and Peptide
Modeling - submitted for review
Papers describing some functionalities of CABS-flex 3.0 method:
Review on CABS-flex applications:
How to report issues with CABS-flex 3.0 server?
In case of any issues, please report them using the CABS-flex 3.0 issue tracker available at
https://github.com/LCBio/cabs-flex/issues.
You can also email us at sekmi@chem.uw.edu.pl