Welcome to PEPstrMOD v2.0

Next-generation tertiary structure prediction of chemically modified and non-natural peptides

PEPstrMOD2 is an updated version of PEPstrMOD for predicting the tertiary structures of chemically modified peptides. The platform expands peptide modeling through support for 428 non-canonical amino acids, 257 post-translational modifications, and 243 terminal modifications. Initial structures generated using AlphaFold2 or ESMFold are subsequently refined through energy minimization and molecular dynamics simulations.

Start Prediction Documentation

Prediction Workflow

Supported Modifications

What Can You Model?

PEPstrMOD2 handles a comprehensive range of chemical modifications in a single unified pipeline.

D-amino acids

D-Residue Isomers

All 20 standard amino acids can be modeled as D-isomers using the AMBER flip command. The resulting structures are subsequently refined through energy minimization and molecular dynamics simulations. Tag: {d}

PTMs

Post-Translational Modifications

Support for 257 ptm modifications including phosphorylation, methylation, acetylation, hydroxylation, and many more. Full AMBER parameterization via ffPTM library. Tag: {ptm:TAG}

Non-natural

Non-Canonical Amino Acids

Support for 428 NCAA modifications including norleucine, beta-amino acids, and other non-natural residues. Parameterized with the ffNCCA force field. Tag: {nnr:TAG}

Cyclization

Cyclic Modifications

N-to-C terminal cyclization and disulfide-bridged peptides. Multiple disulfide pairs supported in a single sequence. Tag: {cyc:N-C} / {cyc:i-j}

Caps

Terminal Modifications

Support for 243 N- and C-terminal modifications, including acetylation (ACE), amide caps (NHE/NME), and numerous chemically modified termini. Tags: {nt:TAG}, {ct:TAG}

Combined

Mixed Modifications

Any combination of the above in a single sequence. e.g., D-residues + PTMs + NCAAs + disulfide + N-cap + C-cap all in one peptide prediction run.

Download Complete Modification List

Features

Why PEPstrMOD2?

Built specifically for the challenges of chemically modified peptide structure prediction.

MAP Format Input

Inline modification tags without separate configuration files. Write sequences exactly as you would annotate them in publications.

ESMFold + AlphaFold

ESMFold + AlphaFold2

Choose between ESMFold for rapid prediction and AlphaFold2 for enhanced accuracy before molecular dynamics refinement.

AMBER Force Fields

Specialized force-field libraries enable accurate treatment of post-translational modifications and non-canonical residues.

MD Refinement

Initial structures generated by ESMFold or AlphaFold2 are refined through energy minimization and molecular dynamics simulations using AMBER force fields.

Analysis Outputs

Generate trajectory analyses, RMSD profiles, clustering results, and energy plots alongside the final refined structure.

Citation

How to Cite

PEPstrMOD2: Jain S., et al. PEPstrMOD2: Next-generation tertiary structure prediction of chemically modified and non-natural peptides. Raghava Lab, IIIT Delhi (2026)

PEPstrMOD: Singh, S., Singh, H., Tuknait, A. et al. PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biol Direct 10, 73 (2015). https://doi.org/10.1186/s13062-015-0103-4