Protein Modelling - CCBB DrDS MolDyn Suite

What We Offer

Our protein modelling platform combines traditional homology modelling with state-of-the-art AI-powered structure prediction. The MODELLER Suite GUI provides a complete workflow from sequence alignment to model evaluation, while AlphaFold Suite offers local GPU-accelerated structure prediction with confidence analysis.

For drug discovery projects, the OpenPharmaco Suite provides pharmacophore model generation and screening capabilities to identify key interaction features for lead optimization.

                        AlphaFold Local Predictions

                        Run AlphaFold2 locally on 3× NVIDIA A30 GPUs (72 GB VRAM) with 384 GB RAM — no external services required. Predict structures for proteins up to 2,500 residues.

AlphaFold Modelling — Local Prediction with GPU Status

Modelling Approaches

Choose the right method for your research needs

Homology Modelling

Template-based modelling using MODELLER. Best when homologous structures with >30% sequence identity are available.

MODELLER

AI Structure Prediction

Deep learning-based folding with AlphaFold2 and ColabFold. Works for any protein sequence including novel folds.

AlphaFold ColabFold

Pharmacophore Analysis

Identify key molecular interaction features for drug design using OpenPharmaco Suite.

OpenPharmaco

Available Tools

Four integrated modules in the web-based modelling platform

AlphaFold Prediction

Local GPU-accelerated AlphaFold2 folding on 3× NVIDIA A30 (72 GB VRAM)
FASTA input via text paste or file upload; support for sequences up to 2,500 residues
Model preset selection (monomer, multimer) and template date cutoff control
Pre-computed structure retrieval by UniProt ID from the AlphaFold Database
Real-time prediction progress with live log and ranked model list on completion

Structure Viewer

Interactive 3D viewer with Cartoon, Stick, Sphere, and Surface rendering modes
Ranked model list (ranked_0 – ranked_4) with one-click switching
pLDDT-colored confidence rendering highlighting high/low confidence regions
Download PDB/CIF structure files directly from the browser

Quality & Confidence Analysis

Overall pLDDT score with per-confidence-tier residue counts (Very Low / Low / Confident / Very Confident)
Per-residue confidence plot with color-filled threshold bands
Intrinsically disordered region (IDR) detection with disorder map
Confidence distribution histogram; all plots exportable as PNG

Structural Analysis

Ramachandran plot — phi/psi dihedral analysis with α-Helix, β-Sheet, and Coil percentages
Cα distance matrix and binary contact map (8 Å cutoff)
Structural metrics: residue count, atom count, molecular weight, secondary structure breakdown
RMSD and GDT-TS model comparison between any two ranked models

Screenshots & Output Gallery

AlphaFold Suite in action — from prediction to analysis

Structure Viewer

Interactive 3D preview with Cartoon/Stick/Sphere/Surface rendering, ranked model list, and one-click launch in PyMOL, ChimeraX, or VMD

AlphaFold Result Analysis — Ramachandran Plot & Structural Metrics

Structural Analysis — Ramachandran Plot

Phi/Psi dihedral analysis with secondary structure metrics: residues, atoms, mol. weight, α-Helix, β-Sheet, Coil percentages

Confidence Distribution

Residue count per confidence tier: Very Low (0–50%), Low (50–70%), Confident (70–90%), Very Confident (90–100%)

Disorder Prediction

pLDDT-based intrinsically disordered region (IDR) detection with disorder map and per-residue confidence plot

Cα Distance Matrix & Contact Map

Residue contact analysis at 8Å cutoff with Cα distance heatmap and binary contact map

Video Demo

Watch a protein modelling workflow walkthrough

Protein Modelling Pipeline Demo

From sequence to validated 3D structure — Coming soon

Ready to Model Proteins?

Sign up to access homology modelling, AlphaFold, and pharmacophore tools

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