Ensemblify

Required entries are marked with an asterisk (*). Hover over the tooltip icons (ⓘ) for more information.

Job Name*

ⓘ Name for generated files and folders.

Input Structure/Sequence*

ⓘ Path to structure/sequence in .pdb or .txt format.
A UniProt accession code can also be provided, in
which case the corresponding structure from the
AlphaFold Protein Structure Database is retrieved.

Do you want to build your full-length structure by joining IDRs with folded domains?

ⓘ Path to FASTA file(s) containing the sequences
of all (folded + disordered) protein domains,
from N- to C-terminal. Can be provided either in
FASTA or Multi-FASTA format.

ⓘ Path to PDB file(s) containing the structures of all
folded protein domains, from N- to C-terminal.
Can be provided as a single PDB file with multiple
MODEL entries.

Size of Ensemble*

ⓘ Size of ensemble to generate (1-100000).

Database(s)*

ⓘ To better utilize your computer's resources,
please add only databases that will be sampled
from in the Sampling Targets section.

ID: Path:

Sampling Target(s)*

ⓘ Any chains or residues indicated must be present in
the input structure. Any database ID indicated must
refer to a database present in the Databases section.
Any non-sampled region will be constrained to its
initial structure.

Chain: Residue Range: Database: Mode:

Output Path*

ⓘ Path to output directory. A directory
named Job Name will be created here.

AlphaFold

ⓘ To use any of the following options, input structure must
be an AlphaFold model, i.e. it must have a B-Factor column
containing the value for each residue's pLDDT.

Do you want to sample residues based on their pLDDT?

ⓘ Residues contained in regions defined in Sampling Targets
will only be sampled if their pLDDT is below a threshold.
If you want to change the pLDDT threshold from the default 70,
check the Advanced Parameters section.

Do you want structure constraints to be applied based solely on the PAE matrix?

ⓘ Any constraints derived from Sampling Targets or defined
in Restraints will be ignored and constraints created from
the given PAE matrix will be used instead. If you want to
customize how these constraints are created, check the
Advanced Parameters PAE section.

ⓘ Path to PAE matrix .json file
from AlphaFold output. A UniProt
accession code can also be
provided, in which case the
corresponding PAE matrix from
the AlphaFold Protein Structure
Database is retrieved.

Restraint(s)

ⓘ Ways to bias sampling towards
desired structural properties.

Secondary Structure Bias ( % )

ⓘ Force the desired secondary structure
element in the desired region on X %
of generated structures.

Contacts

ⓘ Inter-chain contacts present in the input structure (e.g.
dimerization sites) you want to conserve during sampling.

FASPR Path

ⓘ Path to FASPR executable. Defaults to location
defined during Ensemblify installation.

PULCHRA Path

ⓘ Path to PULCHRA executable. Defaults to location
defined during Ensemblify installation.

Core amount

ⓘ Number of processor cores to use. Defaults
to all cores in machine minus 1.

ScoreFunction

ⓘ PyRosetta Score Function .wts weights file,
default or custom, must be defined in
/.../pyrosetta/database/scoring/weights/ .

ID:

ⓘ Default ScoreFunction used is
score0, with only a repulsive
VdW score term.

VdW score term weight:

ⓘ Will only have an effect if the
ScoreFunction has a repulsive
Van der Waals term.

Minimizer

ID:

ⓘ PyRosetta minimization algorithm.

Tolerance:
Maximum iterations:
Final Cycles:

ⓘ Number of final rounds of minimization
to perform on each sampled structure.

Variability

ⓘ Ways to increase conformational sampling
variability between sampled structures.

Variance:

ⓘ New dihedral angle values to insert into flexible
regions are sampled from a Gaussian distribution
centred on the values found in the database and
percentage variance equal to this value.

Monte Carlo Sampler Parameters

Temperature:
Maximum Loops:

Constraints

ⓘ An AtomPairConstraint's value is given by:
f(x) = ((x - x₀) / stdev)²,
where f(x) = 0 for x in [x₀-tol,x₀+tol].
The higher the value, the worse that
residue pair's score will be.

Weight:

ⓘ Weight of the AtomPairConstraint
score term in the ScoreFunction.

Standard deviation:
Tolerance:

Constraints Violation

ⓘ Number of residues whose
AtomPairConstraint's values are
allowed to be above a certain threshold.

Threshold:
Maximum residues:

pLDDT

ⓘ predicted Local Distance Difference Test (pLDDT),
AlphaFold's confidence metric:
- pLDDT > 90: good backbone and sidechain prediction.
- 70 < pLDDT < 90: good backbone prediction.
- 50 < pLDDT < 70: should be treated with caution.
- pLDDT < 50: strong indication of disorder.

Threshold:

ⓘ Only sample residues with pLDDT below this number.

Number of contiguous residues:

ⓘ If residue's pLDDT is below threshold,
sample them only if they make up a
contiguous region of at least this size.

PAE

ⓘ Predicted Aligned Error (PAE) matrix.
If PAE is generally low for a residue pair x, y from two
different domains, it indicates that AlphaFold predicts
well-defined relative positions and orientations for them.

Cutoff:

ⓘ Only consider PAE values below this number.

Flatten cutoff:

ⓘ Any PAE values below this value will
be changed to match flatten value.

Flatten value:

ⓘ Any PAE values below flatten cutoff will
be changed to match this value.

Weight:

ⓘ The stdev of AtomPairConstraints
created from the PAE matrix is
given by error×weight.

Tolerance:

ⓘ The tol of AtomPairConstraints
created from the PAE matrix is
given by this value.

Adjacency Threshold:

ⓘ How far away two residues need to be
to consider their PAE value.

pLDDT Scaling Factor:

ⓘ Constraints between high pLDDT and low
pLDDT residues will be made weaker
through this scaling factor (high
scaling factor -> weaker constraints).