ThermoMPNN

Protein mutation recommendation for increased thermostability

Dieckhaus et al.

TNP (Therapeutic Nanobody Profiler)

Predict nanobody developability

Gordon et al.

TAP2 (Therapeutic Antibody Profiler)

Developability profiler for antibodies

Raybould MIJ et al.

FlashABB

Fast antibody structure, developability, and embeddings

Ellmen et al.

COMPSS Protein Metrics

Score sequences using language model metrics

Johnson et al.

SaProt

Language models for protein property prediction

Su et al.

PEP-Patch

Quantify surface electrostatic potentials

Valentin J. Hoerschinger et al.

SURFMAP

2D projection of protein surface features

Schweke et al.

DeepImmuno

Prediction of immunogenic epitopes for T cell immunity (Class 1)

Guangyuan Li et al.

PredIG

Interpretable T-cell epitope immunogenicity prediction for Class-I pHLA, cancer and pathogen antigens.

Farriol-Duran et al., 2024

TLimmuno

Class II Immunogenicity Prediction

Guangshuai Wang et al.

HLAIIPred

Class II peptide presentation prediction

Haghighatlari et al.

NetSolP

Solubility and usability based on protein language models

Thumuluri V et al.

TEMPRO

Nanobody melting temperature prediction

Alvarez et al.

SaProtΔG

Absolute protein stability (ΔG) prediction from structure

Cho et al.

ESM-IF ΔG

Absolute protein folding stability (ΔG) prediction from structure with ESM-IF

Cagiada et al.

PALM

Protein aggregation propensity prediction

Eschbach et al.

CANYA

Amyloid nucleation propensity prediction

Thompson et al.

PolyXpert

Antibody polyreactivity prediction

DELPHI

Antibody polyreactivity and monomer-purity prediction

Nguyen et al.

Nanobody Polyreactivity

Nanobody (VHH) polyreactivity prediction

Harvey et al.

TemStaPro

Protein thermostability prediction

Pudžiuvelytė et al.

ThermoMPNN-D

Double protein point mutation recommendation for increased thermostability

Dieckhaus et al.

BioPhi

Antibody humanization evaluation and mutation recommendation

Prihoda D et al.

Humatch

Antibody humanization evaluation and mutation recommendation

Chinery et al.

Aggrescan3D

Predict aggregation propensity in protein structures and rationally design protein solubility

Aleksander Kuriata et al.

Deep Viscosity

Viscosity prediction for antibodies

Kalejaye et al.

DeepSP

Viscosity, spatial charge map (SCM) and spatial aggregation propensity (SAP) predictions for antibodies

Lateefat Kalejaye et al.

PepFuNN Peptide Sequence Analysis

Predict properties for peptides

Ochoa R et al.

PLM Crystallization Prediction

Sequence-based crystallization predictor. Mean-ensemble of LightGBM classifiers trained on ESM2 T30-150M and ESM2 T36-3B embeddings.

Mall et al.

deepSTABp

Predict protein melting temperature

Jung et al.

HyperMPNN

Design thermostable proteins

Ertelt et al.

ProteinDPO

Score variants, scan a chain for stabilizing mutations, or design new sequences for a backbone with ProteinDPO, an ESM-IF1 inverse-folding model aligned to experimental stability data.

Widatalla et al.

IPC 2.0

Predict protein isoelectric point and pKa

Kozlowski et al.

N-Linked Glycosylation Prediction

Predict N-Linked Glycosylation sites

Pakhrin et al.

NDPredict

Predict how likely each asparagine (ASN) site in a structure is to deamidate

Jia et al.

Protein Properties

Calculate properties on input sequence/structure

Almeida DS et al.

PeptiVerse

Unified platform for therapeutic peptide property prediction using sequence and SMILES

Zhang et al.

ImmunoSeq

Predict antibody immunogenicity (ADA risk) from paired VH+VL sequences and optimize sequences toward lower immunogenicity, using an interpretable k-mer immune-tolerance method.

Huang et al.

ImmuScope

Predict MHC-II antigen presentation, CD4+ T-cell epitope recognition, and immunogenicity.

Shen et al.

Protein-Sol

Sequence-based protein solubility prediction using compositional features

Hebditch M et al.

SPURS

Protein stability (ddG) prediction from structure for single and multi-mutations

Li et al.