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Deep learning takes on protein folding

In 1972, Anfinsen won a Nobel prize for demonstrating a connection between a protein's amino acid sequence and its three-dimensional structure. Since 1994, scientists have competed in the biannual Critical Assessment of Structure Prediction (CASP) protein-folding challenge. Deep learning methods took center stage at CASP14, with DeepMind's Alphafold2 achieving remarkable accuracy. Baek et al. explored network architectures based on the DeepMind framework. They used a three-track network to process sequence, distance, and coordinate information simultaneously and achieved accuracies approaching those of DeepMind. The method, RoseTTA fold, can solve challenging x-ray crystallography and cryoelectron microscopy modeling problems and generate accurate models of protein-protein complexes.

Science, abj8754, this issue p. 871

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryoelectron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

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Accurate prediction of protein structures and interactions using a three-track neural network - Science Magazine

Recording artiste Tamo J catapulted into the dimensions of reggae-dancehall approximately five years ago and has enjoyed local success since. But the singer-songwriter, who has commanded the attention of his audience, including his peers and critics, has opened up that before now, his mind was not as clear and he wasnt operating at his best. He has since turned to therapy and is grateful for the impact the sessions have made.

Oftentimes, when the word therapy is mentioned to a person, especially a Jamaican, the response is aggressive and defensive. The reaction is usually, Me nah guh nuh shrink. After me nuh mad. Even for a youngster while growing up, we dont see them capitalising on guidance counsellors, but there are many forms of therapy around that people can benefit from using, Tamo J shared in his recent interview with The Weekend Gleaner.

He added: I was impressed by the thought when it was suggested to me because really and truly, people dont usually focus on an artistes mental state. It is more about what we can provide and do. But if an artiste, or any person for that matter, is not in the best state of mind, he or she cant fully function. I know when my mind is clear, I can operate better.

The Change the World artiste decided to face his demons head-on. That included getting to know himself better, getting past the past, and ignoring societys labels for individuals who seek or take the route of getting professional counselling.

He said: Sometimes as human beings, [we] dont realise how important it is to talk to someone. Yes, we have our peers and family members, but I dont think their capabilities are of a professional level or the advice wont come from an unbiased place. Then there is this big stigma around mental health, and the misconception where people immediately associate mental health with mental illness.

Tamo J said that growing up in Jamaica, there have always been conflicting beliefs coming from a learnt and unlearnt place that include how we are raised and the culture. Men are not encouraged to share their emotions, especially not with each other, and he, too, has heard, A why yuh a gwaan suh? Mek yuh a gwaan like one likkle girl, more than once in different environments amongst his male peers.

Males dont learn how to express [themselves]. Instead, we are exposed to constant jeering and criticism. In our culture, we love making fun of our peers, and sometimes there are deep-rooted issues you would be surprised to learn that even the comedians we laugh with, or at, are working through their own mental-health issues, he said. People always have underlying thoughts that affect how we operate daily, without us even knowing, just subconsciously. If we figure out what is happening, then we can function much better.

Tamo Js counselling sessions which have a spiritual and meditational component havent been easy. Still, he is focused on becoming his best self. At the same time, he is a beacon in the music industry simply by sharing that writing and recording music alone is not therapy. Seeking professional guidance helps, and theres no need for the inaccurate stigma. The singer-songwriter revealed that one of the issues he had to work through was love of self.

I literally went through a process of self-discovery, learning to love and embrace myself to the fullest. It is the only way to be, the way you were meant to be. If you are constantly fighting with yourself, for some people, its their physical image. For me, it was much deeper, and that clouds your judgement, Tamo J said.

In the male-dominated music industry, it can often feel like the toughest battleground. With all of us trying to accomplish the same thing, some will start seeing their peers like competition. Now, I see everyone playing them part, and I communicate differently. I have more patience and understand timing better. Its a beautiful thing, and once you dig up what was buried, you cant unsee or unthink it, he continued.

He said that his music has evolved through therapy, helping him create more efficiently and approach his craft with an international (and intentional) mindset because he is able to express himself more freely.

Im able to tap into myself and trust myself more. When writing, an artiste will track back to things people said [up] to two years or more before, and these things can restrict you from expressing ourselves and make you want to try and put everybody elses thoughts into one song instead of trusting yourself. Now, Im taking on a new perspective and trusting myself, Tamo J said.

Tamo J first opened the doors of the music industry by stepping out of the safe space of his bedroom, where he produced his eight-track EP Eccentric, then began working with renowned producers like Mikey Bennett. His singles, Miss Jamaica and Life Too Short, earned him the respect of the industry, and he became a mainstay, writing for artistes like Kranium, Sean Paul, and Denyque. He is currently under the management of Christopher Townsend, attorney-at-law and owner of Genna Storm Productions.

According to Townsend, both emerging and established artistes can benefit from therapy, and he has seen the impact it has had on Tamo J.

Before Tamo J was added to my roster, his songs were of a certain quality high quality, nonetheless but since receiving the counselling, I find the energy is noticeably different, he shared.

The recommendation for an artiste to receive therapeutic counselling has become a regular course of action for the record label to better engage the artiste and industry professionals the label works with. Noting that Tamo Js talent and experience far exceed the local stomping ground, Townsend is comforted by the fact that when it is time for the artiste to get a major breakthrough, he is going to take music to another level because he is capable, physically and mentally, and he is bussing internationally because he has that flavour, that sound, and the look.

stephanie.lyew@gleanerjm.com

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Tamo J is 'digging up deep-rooted issues' in therapy - Jamaica Gleaner

Theater Review

What: Sister Sorry by Alec Wilkinson. Inspired by Alec Wilkinsons The Confession, originally published in The New Yorker. Directed by Joe Calarco

With: Jennifer Van Dyck, Christopher Sears

Who: Barrington Stage Company

Where: Boyd-Quinson Stage, 30 Union St., Pittsfield

When: Through Aug. 29. 7:30 p.m. Tuesdays through Saturdays; 3 p.m. Saturdays and Sundays

Running time: 1 hour, 9 minutes (no intermission)

Tickets: $25-$69

Reservations and information:413-236-8888,barringtonstageco.org

COVID-19 SAFETY PROTOCOL: All patrons must provide proof of vaccination or proof of a negative COVID-19 test (PCR test within 72 hours or an antigen test within 6 hours) and a form of identification.

PITTSFIELD In a recent interview with The Berkshire Eagle, director Joe Calarco said that one of the reasons he was attracted to Alec Wilkinsons new play, Sister Sorry, is its theatricality.

In Calarcos hands and with the remarkably gifted Jennifer Van Dyck in the title, there is more than enough theatricality to go around at Barrington Stage Companys Boyd-Quinson Stage, where Wilkinsons two-character theater work, as he calls it, is being given a vigorously played, brilliantly staged world premiere. The question is whether, given all its theatrical accomplishment onstage from design to performance, it is all worth it; whether, like the true-life article Wilkinson penned for The New Yorker Magazine in 1993, Sister Sorry gives us people who are worth caring about? Im not convinced that it does.

Sister Sorry is a narrative spun by a conceptual artist as she looks back from present day to a time in 1993 when she conceived the idea of creating a conceptual art work she called the Sorry Line. She set up a phone line in her loft apartment and invited people to call anonymously to apologize for or confess to any sins, wrongdoings, misdeeds,crimes they may have committed at any time in their lives. When she had enough, she played them back through a telephone installation she exhibited in a small New York gallery. Afterward, she shut the line down and then restarted it, this time giving callers the opportunity to either leave their own confessions or listen to the confessions of others or both. Needless to say, Sorry Line does not attract a sunny Disneyland crowd.

I come to feel that a third of the calls are true, a third are not, and a third are a mixture of truth and fiction, she says. Someone making a confession is attempting to turn his or her life into a moral tale. A beginning, a middle, and an end. A confession becomes a story, and stories are what give our lives purpose and meaning, correct?

She remains purposefully disengaged above it all, she says. Not superior, just not drawn into the fray, until, that is, there is that one call, the "main event, she labels it, from someone calling himself Jack Flash (played with near hyper-hysteria and intensity by Christopher Sears), who confesses to a brutal crime, a murder, that he may or may not have committed. Not only is Sister Sorry drawn into the fray, she plunges deep into a shadowy abyss in her psyche that is well beyond anything she could have imagined or dared recognize within herself.

Theirs is by no means an easy relationship, especially when Sister Sorry has good reason to believe that Jacks confession may be false.

Jennifer Van Dyck and Christopher Sears star in Barrington Stage's world premiere of "Sister Sorry."

Sister Sorrys safe haven, her territory, is her loft a sizable platform center stage on which are two desk/tables with rolling chairs, two phones. Sears Jack races around the edges of the platform rear, front, sides; eventually literally invading her space, pinning her, at one point, against one of her table/desks, her back to him as she talks to him on the phone. He would be in her face, literally, were she to turn and face him. All at once, the vast, open, exposed confines of Mikiko Suzuki MacAdams evocative set, becomes claustrophobic.

Wilkinsons play poses a range of questions, not the least of them having to do with the nature of art; the relationship between the artist and the work they created. As an artist Im entitled to use the world and its thousand-and-one things any way I care to, any trespass is permissible in pursuit of art, right? Sister Sorry asks rhetorically. But, really, on reflection, what am I an artist of?

Sister Sorry also is interested in what happens when an artist is consumed, taken over, by their creation; when a work of art becomes its own creation.

Also at issue in Sister Sorry is the responsibility we hold for the choices we make in our lives; our responsibility for choices others around us make.

Wilkinson also explores the voyeur instinct within us; that impulse that allows us to look at a horrible car accident, for example, as we drive by, even if we dont want to; that draws our interest to the seedier side of human interaction, our grudging attraction to the tabloid side of life in our culture; the tacit permission that is given that behavior.

In a performance that is as untidy as his characters calculated disheveled appearance, Sears Jack Flash is an exercise in mounting hysteria that robs Jack of a dont-look attraction.

Christopher Sears plays Jack Flash, who calls in to the Sorry Line and confesses to a murder that he may or may not have committed.

On the other hand, as played by the never-less-than-astonishing Van Dyck, there is no lack of clarity, other than her own, in Sister Sorrys obsessive pursuit of Jack; her fascination with him; her surrender to the power she has over her creation, in essence.

Right from a propulsive get-go that never lets go, Van Dycks Sister Sorry catches us with a series of astonishing confessions backstory that establish the wealth of contradictions that define Sister Sorry and which we accept at face value.

Van Dycks Sister Sorry is a supremely smart woman, clearly a loner, who walks the edge of the wild side until one day, with one phone call, she goes over the edge. Her struggle in the 30 years since has been to find her way back.

I see this now, that there is a boundary in the psyche, she says near the end of the play, the mind, the unconscious, whatever you want to call it, that you can approach, but that its not safe to cross. You can never get all the way back. Even if it looks the same, it isnt.

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Review: 'Sister Sorry' plunges deep into a shadowy abyss of the psyche. But are its characters worth caring about? - Berkshire Eagle