Related tools
ThermoMPNN
Predict protein thermostability changes (ΔΔG) for point mutations using a graph neural network. Enables computational saturation mutagenesis screening to identify stabilizing mutations.
Protein stability
Predict protein stability using validated BioPython methods: Instability Index, Aliphatic Index, GRAVY, flexibility analysis, and charge distribution
CANYA
Predict protein aggregation nucleation propensity from amino acid sequences using the Lehner Lab CANYA neural network.
Aggrescan3D
Faithful static-mode Aggrescan3D tool for per-residue aggregation propensity analysis from a single protein structure.
PROPKA 3
Predict pKa values of ionizable groups in proteins and protein-ligand complexes from 3D structure. PROPKA calculates environment-driven pKa shifts for standard ionizable residues, terminal groups, and supported ligand atom types.
Protein-Sol
Predict protein solubility from amino acid sequence using the University of Manchester Protein-Sol method.
AllMetal3D
Predict metal and water binding sites in protein structures using 3D convolutional neural networks (AllMetal3D + Water3D).
SuperWater
Predict protein hydration sites from a structure using a diffusion model with ESM features and a confidence-filtering head.
Molecular descriptors
Compute 200+ RDKit molecular descriptors, drug-likeness rule violations, and structural fingerprints for QSAR, virtual screening, and ML workflows
Protein charge plot
Plot net charge vs pH for protein sequences. Visualize how protein charge changes across pH 0-14 and identify the isoelectric point (pI) where the net charge crosses zero.