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Structure Comparison · November 2020

The results of homology modelling, structure assessment, QMEAN analysis and structures found in SWISS-MODEL Repository can be combined in this new tool.

The consistency of the selected structures is displayed as a chart, variance heatmap and a new colour scheme on the alignment and 3D viewer. Start a comparison now or visit the help page to learn more.

User Annotations in SWISS-MODEL Repository · November 2020

In SWISS-MODEL Repository, we display UniProt sequence features and InterPro domains from categories which are deemed helpful for structural biologists. These are displayed in the alignment and 3D viewer.

You can now upload your own custom annotations at the residue level. Any sequence-level annotation you can think about can now be displayed in 3D. You can for instance visualize mutation site clusters in 3D.

HHblits3 · September 2020

HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins.

We updated the template search from HHblits 2 at this time with the result being template search results now show more remote homologues.

HHblits3 is enabled for all new projects template search and auto model projects.

GMQE (Global Model Quality Estimation) · September 2020

GMQE (Global Model Quality Estimate) aims to predict the expected quality of a protein model when using a certain template for modelling. It combines properties from the target–template alignment and the template structure.

We introduced a multi-layer perceptron approach to combine these properties and increase prediction accuracy.

Notable Updates

SWISS-MODEL has been running for many years, and in October 2018 we celebrated 25 years of SWISS-MODEL.

Major recent updates include a new modelling engine (ProMod3, used since June 2016) and the ability to model heteromers where we also introduced major improvements for modelling of homomers (since November 2017).

Also there have been continuous improvements to our template ranking and the local (per-residue) model quality scores.