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Molecular Visualization & Engineering

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Measurements

0

Residue

--

Chain:-

Type:-

Pocket Analysis

-

Druggability

-

Volume (ų)

-

Residues

Hydrophobic:-

Polar:-

Charged:-

Aromatic:-

Pocket Residues

Mutagenesis

From

Select residue

To

Clash Resolution

Auto-select best rotamer to minimize steric clashes

Superposition

Reference:-

Mobile

Sequence alignment + Kabsch RMSD

Interface Analysis

↔

Salt Bridge Finder

Cutoff (Å)

Mode

Pairs

Surface Residue Finder

Radius (Å)

Max neighbors

Chain

Residues

Motif Finder

Motif (button input only)

Codes: X=any, h=hydrophobic, p=polar, c=charged, +=positive, -=negative, a=aromatic, s=small

Chain

Amino acids

Wildcards

Matches

UniProt Annotations

Interaction Partners

0

Flexibility Analysis

B-factor based flexibility analysis

Flexible (High B-factor)

Rigid (Low B-factor)

2D Ligand Interaction Diagram

Legend

H-Bond

Hydrophobic

π-Stack

Ionic

Ligand

Name:-

Atoms:-

Contacts:-

Residues

Sequence

Ramachandran

Click a point to highlight residue

Total

-

α

-

β

-

Other

-

Helix Sheet Coil ▲ Gly ■ Pro

Disulfide Bonds

0

Ligand Placement

Fetch Molecule

Enter drug name, PubChem CID, or SMILES string

🎯 Dock Ligand

Searches the binding pocket and returns several candidate poses — pick the one to keep.

Poses: 2 credits / pose

⚙️ Advanced docking (manual)

Grid Box Docking

Center X

Center Y

Center Z

Size X (Å)

Size Y

Size Z

Spacing

Flexible ligand (torsion search)

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🏆 Multi-Ligand Screening

Enter molecule names (one per line or comma-separated) · 5 credits / molecule

Live Interaction Monitor

Clashes

0

H-Bonds

0

ΔG est.

-

Fetch a molecule, then 🎯 Dock to get candidate poses and pick the best fit. Manual grid/optimize live under Advanced.

Contact Map

🟦 <8Å🟩 8-12Å🟨 12-15Å⬛ >15Å 🔶 SS

H-Bond Network

0

Click Detect to find hydrogen bonds.

🏆

Ligand Screening Leaderboard

Ranked by binding affinity (ΔG)

Total Screened

0

Best ΔG

-

Drug-Like

0

Target

-

#

Ligand

ΔG (kcal)

MW / LogP

RO5

No ligands screened yet. Use Multi-Ligand Screening to add compounds.

Click row to visualize • RO5 = Lipinski Rule of Five -

Pocket Finder

0

Geometric alpha-sphere cavity detection. Ranks pockets by druggability score (volume, enclosure, composition).

Protein Prep

—

💧 Crystal Waters

Total

-

Conserved

-

Mobile

-

Conserved = B-factor <30 Å² & near polar groups

🔀 Alt Conformations

Residues-

Atoms-

📊 B-Factor Quality

Mean

-

Std

-

Median

-

High-flex residues:

🕳 Missing Residues

-

⚡ Protonation @ pH 7.4

0 HIS

🔗 Disulfide Bonds

-

Code2Fold

Code2Fold

Info

Representation

Color Scheme

Selection Style

Measure

Analysis Tools

Drug Discovery

Measurements

Residue

Pocket Analysis

Mutagenesis

Superposition

Interface Analysis

Salt Bridge Finder

Surface Residue Finder

Motif Finder

UniProt Annotations

Interaction Partners

Flexibility Analysis

2D Ligand Interaction Diagram

Legend

Ligand

Residues

Sequence

Ramachandran

Disulfide Bonds

Ligand Placement

2D Molecule Editor

Contact Map

H-Bond Network

Ligand Screening Leaderboard

Pocket Finder

Protein Prep