PDB IDs

Description: Enter a valid PDB (Protein Data Bank) ID to retrieve the corresponding protein structure directly from the PDB database.

Usage: This option is ideal for users who want to analyze publicly available protein structures without the need to upload their own files.

Input Field: Enter the PDB ID (e.g., 1ABC, 2XYZ) in the provided input box.

Upload PDB Files

Description: Upload your own PDB (Protein Data Bank) file to analyze custom or unpublished protein structures.

Usage: Suitable for users who have modified or proprietary protein structures and wish to visualize their torsion angles.

Supported Formats: Files should be in PDB format (.pdb).

Input Field: Use the "Choose File" button to upload your PDB file from your local machine.

Custom Torsion Angles (φ, ψ)

Description: Define custom torsion angles, specifically phi (φ) and psi (ψ) angles, to generate a tailored Ramachandran plot.

Usage: Beneficial for users who want to manually input specific torsion angles for visualization or comparison with other structures.

Input Field: Use the "Choose File" button to upload your csv file from your local machine.

Custom Torsion Angles (φ, ψ, θ/χ)

Description: Define custom torsion angles, including phi (φ), psi (ψ), and theta/chi (θ/χ) angles, for a more detailed analysis of protein structures.

Usage: Allows users to explore additional torsion angles, such as side-chain angles (θ/χ), for a comprehensive examination of protein conformation.

Input Field: Use the "Choose File" button to upload your csv file from your local machine.

Trajectory

Description: Upload a molecular dynamics trajectory file to analyze the conformational changes of a protein structure over time.

Usage: Ideal for users interested in studying the dynamics of protein folding or other conformational changes during molecular simulations.

Supported Formats: Files should be in formats compatible with MD simulations, such as .xtc or .tpr.

Input Fields: Upload both the trajectory file (.xtc) and the corresponding topology file (.tpr).To analyze the excursion of a residue throughout the simulation, specify the residues using their chain and residue number format, such as A101, A105.Extract PDB files from the specified frame interval in the trajectory file.

Plots

Description: Ramplot can generate both 2D and 3D Ramachandran plots of various types to aid in the analysis of protein structures.

2D Ramachandran Plot (Six Categories): This plot provides a standard 2D visualization of torsion angles, categorized into six types: (a) General case (Ala and the remaining 15 amino acids), (b) Glycine (Gly), (c) Valine/Isoleucine (Val/Ile), (d) Pre-Proline (pre-Pro), (e) Trans-Proline (trans-Pro), and (f) Cis-Proline (cis-Pro). This plot displays torsion angles where green, blue, and red dots represent the favored, allowed, and disallowed regions, respectively.

3D Ramachandran Plot (Six Categories): Similar to the 2D plot, this 3D plot offers a detailed view of the six categories mentioned above. Bars represent the frequency of torsion angles, providing an intuitive understanding of the distribution of angles within each category.

2D Ramachandran Plot (Standard): This plot displays torsion angles where green, blue, and red dots or triangles represent the favored, allowed, and disallowed regions, respectively. Dots represent residues other than glycine, while triangles indicate glycine residues.

3D Ramachandran Plot (Standard): This plot uses bars to show the frequency of torsion angles, offering a clear representation of the distribution across the favored, allowed, and disallowed regions for all residues.

You can choose the plot file type and resolution at the time of input, and download it using the download icon located at the bottom of the plot.

Output Files

Description: Ramplot generates both 2D and 3D Ramachandran plots to assist in the analysis of protein structures. The tool provides several output files that offer various types of information.

Analysis: This file contains statistics on torsion angles categorized into favored, allowed, and disallowed regions, as well as a list of all disallowed region torsion angles.

Result: This file includes details such as PDB ID, Chain, Residue, Residue Number, φ (Phi), ψ (Psi), Omega, Tau, BFactor, χ1, χ2, χ3, χ4, χ5, Disorder, Group, Ramachandran Plot Region (Six Categories), GroupGly, and Ramachandran Plot Region (Standard).

Log: This file contains a log of the program's operations and activities.

You can download it using the download button located at result page.