Prediction Module

Predict Peptide Structure

Enter your MAP-format peptide sequence, configure prediction parameters, and submit your job. Results include the initial predicted structure, energy-minimized structure, MD-refined structure, and optional analysis outputs such as trajectories, clustering, RMSD, and energy profiles.

Peptide Structure
1

Provide Peptide Sequence in MAP format

Enter a single sequence in MAP (Modification and Annotation in Proteins) format. Use inline curly-brace tags to encode modifications.

Quick Examples
Maximum peptide length is 100 residues.
2

Structure Predictor

The backbone structure prediction engine is set as ESMFold by default.

3

AMBER Simulation Environment

Select the solvent environment for the AMBER molecular dynamics simulation and energy minimization.

Hydrophilic (explicit solvent) is recommended for most peptides. Vacuum may be used for speed.
4

Simulation Time

Duration of the AMBER molecular dynamics simulation in picoseconds. Longer simulations provide greater conformational sampling but require additional computation time.

Simulation time (ps): ps
10 ps (fast) 50 ps 100 ps
Recommended settings: 50 ps (default) for most peptides and 100 ps for longer or flexible peptides.
5

Analysis Options Optional

Enable additional analysis outputs to be included alongside the final PDB structure.

Trajectory Analysis
Generates full AMBER trajectory output. Useful for visualizing the MD simulation path. Adds significant file size.
Cluster Analysis
Clusters conformations from the trajectory to identify dominant structural states. Requires trajectory to be enabled.
Energy & RMSD Graphs
Generates plots of potential energy over time and RMSD from the initial structure. Useful for validating simulation convergence.
6

Job Settings Optional

Job prefix / name:
A user-defined identifier for your prediction job.
Live Preview
Detected Modifications
Enter a sequence to see preview…
MAP Format Reference
{d}D-amino acid isomer
{ptm:TAG}Post-translational modification
{nnr:TAG}Non-natural residue replacement
{nt:TAG}N-terminal cap
{ct:TAG}C-terminal cap
{cyc:N-C}Head-to-tail cyclization
{cyc:i-j}Disulfide bond (CYS i–j)
Full documentation →
Common PTM Tags
{ptm:Acet}Acetylation
{ptm:Amin}Amination
{ptm:Butyrl}Butyrylation
{ptm:Croton}Crotonylation
{ptm:Ethyl}Ethylation
{ptm:Fluoro}Fluorination
Common NNR Tags
{nnr:NLE}Norleucine
{nnr:ABA}Alpha-aminobutyric acid
{nnr:NVA}Norvaline
{nnr:T9E}Selenothreonine
Common N-Terminal Tags
{nt:Acet}Acetylation
{nt:NBz}Benzoylation
{nt:Tboc}Butyloxycarboxylation
{nt:DiAc}Diacetylation
Common C-Terminal Tags
{ct:Amid}Amidation
{ct:Nme}N-methyl amide
{ct:Meth}Methylation
{ct:Ethyl}Ethylation
Full modification list →
Citation copied to clipboard