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Sequence Feature Display · July 2021

The display of structures and sequence annotations in SWISS-MODEL Repository was upgraded to improve the navigation. This allows multiple linear tracks of user annotations to be compared simultaneously.

It is now possible to create a link to display all your annotations on a particular entry in Repository making it easier to share with others:

P0DTC2?annotations=alpha,beta,gamma,delta

Model Quality with QMEANDisCo July 2021

The QMEANDisCo global score is now the primary global model quality predictor throughout all SWISS-MODEL services. An intuitive color scheme informs about model quality in a glance.

Quality measures based on QMEAN4 Z-scores are still available but considered deprecated.

As a consequence, we also adapted the quality filter for the SWISS-MODEL Repository model import. A QMEANDisCo global score threshold of 0.5 significantly reduces the likelihood of importing low quality models (global lDDT < 0.5) when compared with the previous QMEAN4 Z-score based criteria.

Membrane Prediction · February 2021

We identify transmembrane proteins in the weekly integration of PDB structures in the SWISS-MODEL Template Library and the SWISS-MODEL Repository.

An implicit solvation model implemented in OpenStructure (mol.alg.FindMembrane) estimates the optimal membrane location for each biounit and performs a classification based on energetic and geometric criteria.

The original algorithm and the used energy function are described by Lomize et al.

The membrane annotations are transfered to models in SWISS-MODEL workspace and SWISS-MODEL Repository.

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.