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Affiliations
1 Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
2 SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
Andrew Waterhouse et al. Nucleic Acids Res. 2018.
Affiliations
1 Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
2 SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
Performance comparison between ProMod-II and…
Performance comparison between ProMod-II and ProMod3 modelling engines. Performance is measured on a…
Performance comparison between ProMod-II and ProMod3 modelling engines. Performance is measured on a benchmark dataset of 250 targets collected during the CAMEO time range 20 October 2017–13 January 2018. For each target, the same template and target-template alignment were used as input for both modelling engines. Each data point represents the difference in model accuracy in terms of all-atom IDDT score. ProMod3 shows a statically significant improvement of 2.65 IDDT points on average (P-value = 1.1E–43) based on paired t-test.
Modelling example of the Ferrodoxin/Ferredoxin-NADP(+)…
Modelling example of the Ferrodoxin/Ferredoxin-NADP(+) Reductase hetero dimeric complex. ( A ) Decision…
Modelling example of the Ferrodoxin/Ferredoxin-NADP(+) Reductase hetero dimeric complex. (A) Decision tree of templates clustered according to their quaternary structure features: oligomeric state, stoichiometry, topology and interface similarity. Three different clusters are formed based on interface similarity between templates. (B) PPI fingerprint analysis of available template structures. The ratio between interface and surface residue entropy (interface conservation, y-axis) is reported as a function of evolutionary distance (sequence identity, x-axis). Templates corresponding to SMTL ID: 1ewy.1 (in blue) and SMTL ID: 1gaq.1 (in green) show the typical conservation pattern observed for biologically relevant interfaces, with stronger conservation signal in the sequence identity range between 40 and 60%. Considering also remote homologs (below 40% sequence identity), only the interface in template SMTL ID: 1gaq.1 is deemed as conserved (interface/surface conservation ratio below zero). Template corresponding to SMTL ID: 3w5u.1 (in red) displays an interface/surface conservation ratio close to zero, as observed in crystal contacts/artefacts. (C) Structure superposition of available templates. Each template is coloured according to same colouring scheme of Figure 2A and B. Templates corresponding to SMTL ID: 1ewy.1 (in blue) and 1gaq.1 (in green) show similar arrangement of FNR and Fd in the complex. Template SMTL ID: 3w5u.1 (red) shows a different localization of the Fd moiety. Cross-linked cysteines are shown in sticks. (D) Structure superposition between model and native structure of the root FNR:Fd complex. The model is coloured according to its local quality using a colour gradient from blue (high quality) to red (low quality) as measured by all-atom IDDT score. The native structure of the complex is shown in light gray.
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When Xueli was a baby her parents left her on the ground outside an orphanage. In China, albinism is seen by some as a curse.
The rare genetic condition causes a lack of pigment which makes Xueli's skin and hair very pale and also makes her extremely sensitive to sunlight.
But looking different led Xueli to her modelling career. Now aged 16, she has graced the pages of Vogue and fronted campaigns for top designers.
This is her story as told to Jennifer Meierhans.
The staff at the orphanage named me Xue Li. Xue means snow and Li means beautiful. I was adopted when I was three and went to live with my mum and sister in the Netherlands. My mother said she could not think of a more perfect name and she thought it was important to keep a reference to my Chinese roots.
But in some countries in Africa, they are hunted, their limbs may be cut off or they are killed. Witch doctors use their bones to make medicines as people believe these can cure diseases but of course this is not true, these beliefs are myths. I'm lucky I was only abandoned.
My birth parents didn't leave any information about me so I don't know when my birthday is. But about a year ago, I had an X-ray of my hand to get a more accurate idea of age and the doctors thought 15 was about right.
I fell into modelling by chance when I was 11. My mum was in contact with a designer who was originally from Hong Kong. She has a son with a cleft lip and she decided that she wanted to design very fancy clothes for him so people would not always just stare at his mouth. She called the campaign "perfect imperfections" and asked if I wanted to join her fashion show in Hong Kong. That was an amazing experience.
After that, I was invited on a couple of photo shoots and one of them was for Brock Elbank at his studio in London. He published my portrait on Instagram. Zebedee Talent modelling agency got in touch and asked if I wanted to join them in their mission to get people with disabilities represented in the fashion industry.
One of the pictures Brock shot of me was featured in Vogue Italia's June 2019 edition with Lana del Rey on the cover. At the time, I didn't know what an important magazine it was and it took me a while to realise why people got so excited about it.
In modelling, looking different is a blessing not a curse and it gives me a platform to raise awareness of albinism.
The Kurt Geiger campaign is a really great example of how they let me show my difference. They allowed me to style and direct the shoot with my sister because coronavirus restrictions meant the photographer could not be in the studio. It meant I could express myself in whatever way I wanted and I'm really proud of the results.
There are still models who are like eight foot two and skinny but now people with disabilities or differences are featured more in the media and this is great - but it should be normal. Models with albinism often get stereotyped in shoots to depict angels or ghosts and it makes me sad. Especially because it perpetuates those beliefs that endanger the lives of children with albinism in countries such as Tanzania and Malawi.
Albinism affects the production of melanin - the pigment that gives eyes, skin and hair its colour
People with albinism have a reduced amount of melanin or no melanin at all and often have very pale hair, skin and eyes
The prevalence of albinism varies across the world. About one in every 17,000 people in the UK has some form of albinism, the NHS estimates
The term "person with albinism" is preferred to "albino", which is often used in a derogatory way
You can learn more about albinism from the United Nations Human Rights Commission.
My albinism means I only have eight to 10 per cent vision and I can't look directly at light as it hurts my eyes. Sometimes if it's too bright on a shoot I will say "May I close my eyes or can you make the light softer?" Or I'll say "OK, you can do three pictures with my eyes open with the flash and no more."
At first they might think it's hard but when they take the first picture they are like "Wow" and they are really happy with the results. My management say to clients "If you can't arrange that you can't have Xueli." It's important to them that I feel comfortable.
People tell me my visual impairment gives me a different perspective and I see details that others do not observe. It also makes me care less about the traditional view of beauty. Maybe because I cannot see everything properly I focus more on people's voices and what they have to say. So their inner beauty is more important to me.
I love modelling because I like meeting new people, practising my English and seeing that people are happy with my pictures. I want to use modelling to talk about albinism and say it's a genetic disorder, it's not a curse. The way to talk about it is to say "a person with albinism" because being "an albino" sounds as if it defines who you are.
People say to me that I have to accept things in my past but I think that's not the case. I believe you need to see what's happened and understand why but not accept it. I'm not going to accept that children are being murdered because of their albinism. I want to change the world. 
I want other children with albinism - or any form of disability or difference - to know they can do and be anything they want. For me, I'm different in some ways but the same in others. I love sport and climbing and I can do it as well as anyone else. People might say you can't do things but you can, just try.
Kurt Geiger: People Empowered - Xueli
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