Missense3D | Structural Bioinformatics Group

Welcome to the Missense3D suite of resources, developed by Professor Michael Sternberg's Group and Dr Alessia David's Group. The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates.

Resources

Missense3D predicts the structural changes introduced by an amino acid substitution. It is applicable for the analyse both experimental coordinates and predicted structures.

Missense3D-TM produces predictions regarding the structural impact of missense variants on transmembrane protein structure. Missense3D-TM provides an overall binary prediction as structurally ‘Damaging’ or ‘Neutral’ based on structural features like ‘breakage of a salt bridge’ and ‘cavity altered’.

Databases

Missense3D-DB is a database of precomputed structural predictions for ~4M human missense variants.

Missense3D-PTMdb is a comprehensive resource which allows users to explore millions of variants, post-translational modifications (PTMs), and topology information, if any, for the collection of canonical proteins within the human proteome (~20,000). Users can visualize these features on a 3D AlphaFold model for their protein of interest.

Missense3D-αDB is a database of pre-computed Missense3D predictions of naturally-occurring missense variants evaluated on AlphaFold models across the human proteome.

Other Resources

PHYRE 2.2 A user-friendly web server for predicting protein 3D structure from amino acid sequence, using homologous templates from the PDB—covering both apo and holo forms when available—and the closest AlphaFold2 model. Users can also upload their own template structures.

A utility to check if the sequence of a protein structure is consistent with the current UniProt entry sequence

The GWYRE resource contains modeled and experimentally determined structures of human proteins and protein complexes, annotated by phenotypic effects of genetic mutations. Future releases will contain proteins and protein complexes from other organisms, extended search options, and advanced scoring of residue mutations

Legacy Versions

Missense3D predicts the structural changes introduced by an amino acid substitution. It is applicable for the analyse both experimental coordinates and predicted structures.

Missense3D-PPI predicts the structural changes introduced by an amino acid substitution affecting Protein-Protein interfaces. Use this option if your protein structure has multiple chains and the mutation may occur across the interface. It is applicable for the analyse both experimental coordinates and predicted structures.