Documentation

Help & User Guide

Learn how to prepare MAP-format peptide sequences, configure prediction settings, submit jobs, and interpret PEPstrMOD2 outputs.

Getting Started

How to Use PEPstrMOD2

Follow the workflow below to predict and refine the tertiary structure of natural, modified, cyclic, and non-natural peptides using PEPstrMOD2.

1

Enter MAP-Format Peptide Sequence

Input your peptide sequence using the MAP (Modification and Annotation in Proteins) format. PEPstrMOD2 supports natural amino acids, D-amino acids, post-translational modifications (PTMs), non-natural residues (NCAAs), terminal modifications, disulfide bonds, and cyclic peptides. A complete list of supported modifications can be found in the user list file.

MAP sequence input
2

Select the Initial Structure Predictor

The PEPstrMOD2 web server uses ESMFold to generate the initial peptide structure prior to molecular dynamics refinement. The standalone version of PEPstrMOD2 additionally supports AlphaFold2 (via ColabFold).

Predictor Selection Screenshot
3

Choose the Simulation Environment

Select the molecular dynamics refinement environment. Available options include vacuum simulations and hydrophilic simulations using explicit TIP3P water molecules.

Environment Selection Screenshot
4

Set the Simulation Duration

Choose the molecular dynamics production time for refinement. Longer simulations can improve structural sampling but require additional computational resources and execution time.

Simulation Time Screenshot
5

Configure Analysis Options (Optional)

Optionally enable additional analysis outputs to be generated alongside the refined peptide structure. Users can choose to save the molecular dynamics trajectory, perform cluster analysis to identify dominant conformations, and generate energy and RMSD plots for evaluating simulation stability. These analyses provide further insight into the refinement process but may increase the output file size and execution time.

Analysis Options Screenshot
6

Configure Job Settings and Submit

Optionally specify a job name to identify your prediction and use it as the prefix for the generated output files. Once all prediction parameters have been configured, click Run PEPstrMOD2 Analysis to start the structure prediction and molecular dynamics refinement workflow. The Clear All button can be used to reset all input fields and restore the default settings.

Job Settings and Submission Screenshot
7

View and Download Results

Once the prediction is complete, users can visualize and download the initial predicted structure, minimized structure, MD-refined structure, analysis plots, and trajectory files generated during the simulation workflow.

Results Page Screenshot
FAQs

Frequently Asked Questions

What types of peptides can be modeled using PEPstrMOD2?

PEPstrMOD2 supports natural peptides, D-amino acid containing peptides, post-translationally modified peptides, non-natural residues, terminal modifications, cyclic peptides, and disulfide-bonded peptides.

What sequence format does PEPstrMOD2 accept?

PEPstrMOD2 accepts peptide sequences in MAP (Modification and Annotation in Proteins) format. MAP annotations can describe modifications, non-natural residues, terminal modifications, cyclization, and disulfide bonds.

Which structure prediction methods are available?

The web server currently uses ESMFold for initial structure prediction. The standalone version available through GitHub and Docker supports both ESMFold and AlphaFold2 (via ColabFold).

What simulation environments are available?

PEPstrMOD2 currently supports vacuum and hydrophilic (TIP3P water) environments for molecular dynamics refinement.

Can I download the generated structures?

Yes. Predicted structures, refined structures, and associated output files can be downloaded from the results page after successful completion of a job.

Are molecular dynamics trajectories available?

Yes. Trajectory files generated during molecular dynamics refinement can be downloaded for further analysis and visualization.

How long does a prediction take?

Runtime depends on peptide length, prediction method, simulation time, and current server workload. Molecular dynamics refinement is generally the most time-consuming step of the workflow.

Can I use PEPstrMOD2 for cyclic peptides?

Yes. Both head-to-tail cyclization and disulfide-bond-based cyclization can be specified through MAP-format annotations.

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Underlying prediction methods

PEPstrMOD2 supports AlphaFold2 (via ColabFold ) and ESMFold for generating initial peptide structures prior to molecular dynamics refinement. The current web server uses ESMFold, while the standalone GitHub and Docker versions support both ESMFold and AlphaFold2 (via ColabFold).