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‘Stunning advance’ on ‘protein folding’: A 50-year-old science problem solved and that could mean big things – USA TODAY

A breakthrough on protein folding could unlock new possibilities into disease understanding and drug discovery, among other fields.(Photo: DeepMind)

Anew discovery about "protein folding" could unlock a world of possibilities into the understanding ofeverything from diseases to drugs, researchers say.

The breakthrough that is sending ripples of excitement throughthe science and medical communities this week deals with theshapestiny proteins in our bodies essential to all life fold into.

The so-called "protein-folding problem" has puzzled scientists for five decades, and the discovery this week from the London-based artificial intelligence lab DeepMind has been heralded as a major milestone.

"This computational work represents a stunning advance on the protein-folding problem, a 50-year old grand challenge in biology," said Venki Ramakrishnan, president of the U.K.'s Royal Society. "It has occurred decades before many people in the field would have predicted. It will be exciting to see the many ways in which it will fundamentally change biological research.

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Proteins are essential to life, supporting practically all of its functions, according to DeepMind, which is owned by Google. They are large, complex molecules, made up of chains of amino acids, and what a protein does largely depends on its unique 3D structure.

The ability to predict protein structures accurately enables a better understanding of what they do and how they work.

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When proteins are translated from their DNA codes, they quickly transform from a non-functional, unfolded state into their folded, functional state. Problems in folding can lead to diseases such asAlzheimer's and Parkinson's.

The companys breakthrough essentially means that it figured out how to use artificial intelligence to deliver relatively quick answers to questions about protein structure and function that would take many months or years to solve using currently available methods, according to STAT News.

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DeepMinds program, called AlphaFold, outperformed about 100 other teams in a biennial protein-structure prediction challenge called CASP, short for Critical Assessment of Structure Prediction, according to the journal Nature.

We have been stuck on this one problem how do proteins fold up for nearly 50 years," said University of Maryland professor John Moult, co-founder and chair of CASP. "To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts wondering if wed ever get there, is a very special moment.

Researchers from DeepMind plan to publish their results in a peer-reviewed journal in the near future.

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New AI That Predicts Shape of Proteins Could Solve 50-Year Problem – The Great Courses Daily News

By Jonny Lupsha, News Writer

According to The New York Times, a lab in London may have developed an artificial intelligence that can do a years-long task in less than a day, solving a longstanding problem of biology. For biologists, identifying the precise shape of a protein often requires months, years, or even decades of experimentation, the article said. It requires skill, intelligence, and more than a little elbow grease.

Now, an artificial intelligence lab in London has built a computer system that can do the job in a few hoursperhaps even a few minutes.

The article said that the laboratory in question, DeepMind, analyzes a string of amino acids that make up a protein and then rapidly and reliably predicts its shape. But why is that so important?

The study of folding proteins began in the 1950s with American biochemist Christian Anfinsen playing a key role.

The first experiments began by taking a protein out of the cell, unfolding it, and then seeing if it could refold in a test tube, independent of any cellular factors, said Dr. Kevin Ahern, Professor of Biochemistry and Biophysics at Oregon State University. The protein Christian Anfinsen picked was the enzyme ribonuclease A, also known as RNase, which turned out to be a serendipitous choice. RNase is relatively small as proteins goabout 100 amino acidsand it is also extraordinarily stable.

Dr. Ahern said that most enzymes are very sensitive to changes in temperature or pH balance, but RNase is not. Anfinsen showed that once an enzyme is unfolded, its capable of refolding outside the cell. His work earned him the 1972 Nobel Prize for Chemistry. Dr. Ahern also said that this process is called renaturation because the protein gets returned to its native or natural state.

Humanity has been studying protein folding for over 60 years. What happens when proteins fold incorrectly? As it turns out, nothing good.

These are the so-called prion diseases, also known as transmissible spongiform encephalopathies or TSEs, Dr. Ahern said. Prion diseases affect humans and other animals. They are a group of degenerative disorders that affect the brain, creating microscopic holes that make the tissue look like a sponge.

He also said that one of the best-known prion diseases is bovine spongiform encephalopathy, also known as Mad Cow Disease. Animals that had it would exhibit behaviors that were consistent with neurological damage, and finding a common cause among them was difficult.

Stanley Prusiner at the University of California at San Francisco ultimately identified the infectious agent as a proteina proteinaceous infectious article he called a prion, Dr. Ahern said. That a protein could be infectious by itself was unheard of at the time. And [it] turned out to be a cellular protein found on the membrane of healthy cells; though its function to this day remains uncertain.

Protein misfolding causes several serious diseases and helps explain why the study of protein folding matters so much.

This article was proofread and copyedited by Angela Shoemaker, Proofreader and Copy Editor for The Great Courses Daily.

Dr. Kevin Ahern contributed to this article. Dr. Ahern is a Professor of Biochemistry and Biophysics at Oregon State University (OSU), where he also received his PhD in Biochemistry and Biophysics.

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Lattman, Liu, Morrow and Ruhl elected AAAS fellows – UB Now: News and views for UB faculty and staff – University at Buffalo Reporter

Your Colleagues

UBNOW STAFF

Published November 30, 2020

Four UB professors have been elected fellows of the American Association for the Advancement of Science (AAAS), the world's largest general scientific society and publisher of the journal Science.

The honor is bestowed on AAAS members by their peers for their scientifically or socially distinguished efforts to advance science applications. The UB faculty members were among 489 members to receive the prestigious distinction this year.

The new UB fellows include:

AAAS fellows will be recognized in the journal Science on Nov. 27. An induction ceremony will be held during the virtual AAAS Fellows Forum on Feb. 13.

Eaton Lattman (biological sciences)

Lattman was honored for his distinguished contributions in scholarship, education and leadership in the fields of molecular biophysics and structural biology.

A prolific researcher in crystallography and biophysics, Lattman has focused on protein folding and on development and improvement of methods in protein crystallography. He has pioneered the emerging field of using X-ray free electron lasers to study biological and nonbiological processes.

Lattman spent nearly his entire academic career at Johns Hopkins University, as professor of biophysics in both the School of Medicine and the Krieger School of Arts and Sciences, where he also served as dean of research and graduate education. He played a key role in establishing the Hopkins Institute for Biophysical Research.

In 2008, Lattman came to Buffalo to serve as chief executive officer at Hauptman-Woodward Medical Research Institute. He joined the UB Department of Structural Biology in 2009.

In 2013, he was instrumental in the awarding of a $25 million U.S. National Science Foundation grant to UB and its partners to establish BioXFEL, an X-ray laser science center, to transform the field of structural biology. It was UBs first NSF Science and Technology Center Grant. Lattman was named director and led the national consortium until 2017. Under his direction, the consortium made significant progress in refining X-ray laser techniques to study biological processes and innovating new approaches to use these methods to advance materials science and other nonbiological disciplines as well. He continues to serve as a member of the BioXFEL steering committee.

Xiufeng Liu (education)

Liu was recognized for his distinguished contributions to the fields of science education research, and communicating and interpreting science to the public.

Liu is renowned for his scholarship on measuring and evaluating student achievement in science, technology, engineering and math (STEM). He served as the inaugural director of UBs Center for Educational Innovation, with a mission to improve university teaching, learning and assessment.

He also strives to increase scientific literacy among members of the public, and inspired a program at UB called Science and the Public that prepares museum curators, zoo directors, pharmacists and other informal science educators to teach science to a general audience, including by engaging in activities and debates related to science.

Liu has received more than $18 million in research funding, and published more than 100 academic articles and 10 books. He received a doctorate in science education from the University of British Columbia and a masters degree in chemical education from East China Normal University.

Janet Morrow (chemistry)

Morrow was honored for her distinguished contributions to the field of inorganic complexes and their biomedical applications, particularly for magnetic resonance imaging contrast agents and for nucleic acid modifications.

Morrow is an expert in bioinorganic chemistry, with a wide range of innovations and publications in the field. The central theme of her research is the synthesis of inorganic complexes for biomedical diagnostics, sensing or catalytic applications. Focus areas include research and development of novel MRI contrast agents, yeast cell labeling with metal complex probes to track infections, and bimodal imaging agents. Morrow is also an inventor and entrepreneur, having co-founded Ferric Contrast, a startup that is developing iron-containing MRI contrast agents.

She is a recipient of the Jacob F. Schoellkopf Medal presented by the Western New York section of the American Chemical Society, the UB Exceptional Scholar Award for Sustained Achievement, the National Science Foundation Award for Special Creativity and the Alfred P. Sloan Research Fellowship. Morrow holds a doctorate in chemistry from the University of North Carolina at Chapel Hill and a bachelors degree in chemistry from the University of California, Santa Barbara.

Stefan Ruhl (dentistry and oral health sciences)

Ruhl was recognized for his distinguished contributions to the field of oral biology, particularly for work on glycan-mediated microbial adhesion in the oral cavity.

Ruhl is an internationally renowned expert on saliva, oral bacteria and the oral microbiome. His research attempts to unravel the roles that saliva and microorganisms play in health, including in adhesion to the teeth and surfaces of the mouth, defense against pathogens and colonization of the oral cavity. He investigates the molecular mechanisms of microbial binding to glycans, a common but little understood class of biomolecules that help bacteria attach to host surfaces, including those in the mouth. The goal of his lab is to harness tools that ultimately help scientists examine how the microorganisms bind to glycans in the mouth to form dental biofilms more commonly known as plaque increasing the risk for cavities and periodontal disease.

He was among the first researchers to catalogue the human salivary proteome, which is the entirety of proteins present in saliva and in salivary gland ductal secretions. Ruhl has led or participated in recent studies that have identified how saliva is made, tracing each salivary protein back to its source. He also discovered that 2 million years of eating meat and cooked food has led humans to develop a saliva that is now starkly different from that of chimpanzees and gorillas, our closest genetic relatives. This seminal discovery has resulted in collaborative projects exploring saliva to understand the factors that helped shape human evolution and, in particular, the evolution of the human mouth. These evolutionary projects identified a starch-digesting enzyme called amylase in the saliva of dogs and various other starch-consuming mammals, and through analysis of a salivary mucin protein found genetic evidence that humans may have mated with a ghost species of archaic humans.

Ruhl received the 2020 Distinguished Scientist Award in Salivary Research and the 2014 Salivary Researcher of the Year award from the International Association for Dental Research, as well as the UB Exceptional Scholar Award for Sustained Achievement. He holds a doctor of dental surgery degree and a doctoral degree in immunology from Georg-August University of Gttingen.

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Israeli Scientists Kill Cancer With Revolutionary DNA-Altering Treatment (with VIDEO) – The Media Line

Tel Aviv University researchers use tiny molecular scissors to target aggressive metastatic cancer cells

Israeli scientists have developed a cutting-edge nanotechnology system that can destroy cancerous cells in mice.

The Tel Aviv University team of researchers pioneered a treatment method that is so precise, it is almost as if tiny molecular scissors were being used to kill the cancer.

We developed a delivery system for these molecular scissors that can specifically reach tumor cells while leaving normal cells intact, Dr. Daniel Rosenblum, a postdoctoral fellow from the Laboratory of Precision NanoMedicine at the Shmunis School of Biomedicine and Cancer Research at Tel Aviv University, told The Media Line.

By cutting their DNA in specific genes that are responsible for cell division or cell survival, we basically neutralize them and they die from the treatment, he said. The system we developed is based on the Cas9 CRISPR protein in a [messenger] RNA format.

The process, known as CRISPR genome editing, allows researchers to alter DNA sequences. Specifically, scientists at the university created what is known as CRISPR-LNPs, a lipid nanoparticle delivery system that carries a genetic messenger (known as messenger RNA), along with a navigation system that can recognize cancerous cells.

The findings of the peer-reviewed research were published last month in the Science Advances journal.

This is the first study in the world to prove that the CRISPR genome editing system can be used to treat cancer in a living animal effectively,said Prof. Dan Peer, vice president for Research and Development at Tel Aviv University and head of TAUs Laboratory of Precision NanoMedicine.

The idea there is to take the cells from the patients, edit them in a plate outside the body and then inject them back into the patient, he told The Media Line. We believe that this could be expanded to much more than just the two models that we have tried.

So far, researchers at Tel Aviv University have tested the technology on mice and have observed no adverse reactions. This stands in contrast to chemotherapy, which kills both cancerous and healthy cells.

The CRISPR-LNPs were tested on glioblastoma tumors, an extremely aggressive type of brain cancer that has a five-year survival rate of only 3%. In addition, the researchers tested the system on metastatic ovarian cancer, a major cause of death among women and the most lethal cancer in the female reproductive system.

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For the glioblastoma tumors, the treatment was found to double the average life expectancy of mice and improve their overall survival rate by about 30%. For ovarian cancer, the overall survival rate rose by a whopping 80%.

When we started we thought this was a science-fiction approach but basically it works, at least in the animal models that we have tried

We envision that we can simply inject [the treatment] into the body and because of the GPS they can find their way to the tumor, Anna Gutkin, a doctoral student in the laboratory, told The Media Line. We encountered several hurdles in the development of this technology but its exciting to work on this. It really opens new avenues for us to develop novel therapies.

Aside from its potentially revolutionary impact on future cancer treatments, the technology also opens the door for treating rare genetic diseases and viral diseases such as AIDS, according to the researchers. A similar technology based on messenger RNA currently is being used by Pfizer (BioNTech) and Moderna for their COVID-19 vaccines.

Our system is a bit more sophisticated both from the materials they are created from [and] we also gave it a GPS system, which is pretty unique, Rosenblum noted.

In the future, Peer and his team hope to test the groundbreaking technology on larger animal models. Human trials are expected to begin in about two years.

Because of the coronavirus crisis we have witnessed how fast new approaches could be translated into the clinic, Peer said.

When we started we thought this was a science-fiction approach but basically it works, at least in the animal models that we have tried, he concluded.

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Cancer Nanomedicine Market Size, Comprehensive Analysis, Development Strategy, Future Plans and Industry Growth with High CAGR by Forecast 2026 |…

Global Cancer Nanomedicine Market Survey Research Report

The Global Intelligence Insights added a new report Global Cancer Nanomedicine Market: Global Industry Analysis, Size, Share, Growth, Trends, and Forecast, 2016 2024 in its database, which provides an expert and in-depth analysis of key business trends and future market development prospects, key drivers and restraints, profiles of major market players, segmentation and forecasting.

Market Overview:

Cancer Nanomedicine Market to grow from USD 761.85 billion in 2016 and reach USD 918.74 billion by 2020, growing at a CAGR of 4.8% during the forecast period.

The global Cancer Nanomedicine Market report offers a complete overview of the Cancer Nanomedicine Market globally. It presents real data and statistics on the inclinations and improvements in global Cancer Nanomedicine Markets. It also highlights manufacturing, abilities & technologies, and unstable structure of the market. The global Cancer Nanomedicine Market report elaborates the crucial data along with all important insights related to the current market status.

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Top Key Players: Abraxis BioScience,Access Pharmaceuticals,Alnylam Pharmaceuticals,Arrowhead Research,BIND Biosciences,Epeius Biotechnologies,Nanobiotix,NanoCarrier,Nippon Kayaku,Samyang,Takeda Pharmaceutical

The main goal for the dissemination of this information is to give a descriptive analysis of how the trends could potentially affect the upcoming future of Cancer Nanomedicine market during the forecast period. This markets competitive manufactures and the upcoming manufactures are studied with their detailed research. Revenue, production, price, market share of these players is mentioned with precise information.

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5 United States

6 Europe

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13 Market Forecasts 2019-2025

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Nanomedicine Market 2019 Global Outlook, Research, Trends and Forecast to 2025 – The Haitian-Caribbean News Network

Nanomedicine Market Forecast 2020-2026

The Global Nanomedicine Market research report provides and in-depth analysis on industry- and economy-wide database for business management that could potentially offer development and profitability for players in this market. This is a latest report, covering the current COVID-19 impact on the market. The pandemic of Coronavirus (COVID-19) has affected every aspect of life globally. This has brought along several changes in market conditions. The rapidly changing market scenario and initial and future assessment of the impact is covered in the report. It offers critical information pertaining to the current and future growth of the market. It focuses on technologies, volume, and materials in, and in-depth analysis of the market. The study has a section dedicated for profiling key companies in the market along with the market shares they hold.

The report consists of trends that are anticipated to impact the growth of the Nanomedicine Market during the forecast period between 2020 and 2026. Evaluation of these trends is included in the report, along with their product innovations.

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The Report Covers the Following Companies:CombimatrixAblynxAbraxis BioscienceCelgeneMallinckrodtArrowhead ResearchGE HealthcareMerckPfizerNanosphereEpeius BiotechnologiesCytimmune SciencesNanospectra Biosciences

By Types:Quantum dotsNanoparticlesNanoshellsNanotubesNanodevices

By Applications:Segmentation encompasses oncologyInfectious diseasesCardiologyOrthopedicsOthers

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By Regions:

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Years Considered to Estimate the Market Size:History Year: 2015-2019Base Year: 2019Estimated Year: 2020Forecast Year: 2020-2026

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Nanomedicine Market 2020 by Industry Growth And Competitive Landscape Trends, Segmentation SRI International (US), Aditech Ltd. (UK), Anviz Global,…

Introduction:

This exclusive research report on global Nanomedicine market initiated by Orbis Pharma Reports is an demonstrative replica of diverse market relevant factors dominant across historical and current timelines. The report is anticipated to aid market players willing to upscale their business models and ROI. The report carries out a deep analytical study to identify and understand the potential of core factors that stimulate high end growth. In this report, expert research analysts at Orbis Pharma Reports categorically focus on the pre and post pandemic market conditions to equip readers with ample cues on market progression based on which frontline vendors and other contributing players can successfully design and deploy accurate business decisions and apt growth strategies to secure a healthy footing amidst stringent market competition, fast transitioning regulatory framework and vendor preferences.

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Major Company Profiles operating in the Nanomedicine Market:

CIC biomaGUNESwedNanoTechBiotechrabbitChemConnectionLTFNAffilogicIstec CNREndomagneticsCarlina technologiesVicomtechVITO NVGrupo PraxisCIBER-BBNGIMACTecnaliaBraccoCristal TherapeuticsTeknikerFraunhofer ICT-IMMBergmannstrostMaterials Research CentreContiproDTIIMDEA

Scope:

The report also includes specific details on core developments such as pricing strategies and manufacturer investments towards selecting growth appropriate business decisions, understanding core methodologies, market size, dimensions as well as share, and market CAGR inputs and investments that collectively illuminate growth favorable route in global Nanomedicine market.Based on market research endeavors and gauging into past growth milestones, seasoned in-house researchers at Orbis Pharma Reports are suggesting an impressive comeback of global Nanomedicine market, significantly offsetting the implications of the global pandemic and its aftermath.

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Nanomedicine Market Product Type:

Type 1Type 2Type 3

Nanomedicine Market Application:

Application 1Application 2Application 3

Segmentation by Type and ApplicationThe end-use application segment is thoroughly influenced by fast transitioning end-user inclination and preferences. Product and application-based segments clearly focus on the array of novel changes and new investments made by market forerunners towards improving product qualities to align with end-use needs. Additionally, this report by Orbis Pharma Reports also includes a dedicated section on various categorization of the market based on product type and diversification. Each of the product and service offerings are maneuvered to undergo rapid transitions to improve growth scope and investment returns in the coming years.

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1.The report by Orbis Pharma Reports outlines crucial attributes of the global Nanomedicine market with detailed understanding of major innovations and events, also highlighting growth plot chalked by leading players2.A decisive overview of macro and micro economic factors have also been highlighted in the report to understand major influences and drivers3.An in-depth impression of crucial technological milestones and a value-based and volume-based output of the same have also been pinned in the report.4.Rife predictions on segment performance and opportunity analysis have also been minutely addressed in the report to decipher growth process and futuristic possibilities.

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At Orbispharma we curate the most relevant news stories, features, analysis and research reports on the important challenges undertaken by the pharmaceutical and related sectors. Our editorial philosophy is to bring you sharp, focused and informed perspective of industries, the end users and application of all upcoming trends into the pharma sector. Orbispharma believes in conversations that can bring a change in one of the most crucial economic sectors in the world. With these conversations we wish our customers to make sound business decisions with right business intelligence.

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AI system solves 50-year-old protein folding problem in hours – Livescience.com

An artificial intelligence company that gained fame for designing computer systems that could beat humans at games has now made a huge advancement in biological science.

The company, DeepMind, which is owned by the same parent company as Google, has created an AI system that can rapidly and accurately predict how proteins fold to get their 3D shapes, a surprisingly complex problem that has plagued researchers for decades, according to The New York Times.

Figuring out a protein's structure can require years or even decades of laborious experimentation, and current computer simulations of protein folding fall short on accuracy. But DeepMind's system, known as AlphaFold, required only a few hours to accurately predict a protein's structure, the Times reported.

Related: Why does artificial intelligence scare us so much?

Proteins are large molecules that are essential for life. They are made up of a string of chemical compounds known as amino acids. These "strings" fold in intricate ways to create unique structures that determine what the protein can do. (For example, the "spike" protein on the new coronavirus allows the virus to bind to and invade human cells.)

Nearly 50 years ago, scientists hypothesized that you could predict a protein's structure knowing just its sequence of amino acids. But solving this "protein folding problem" has proved enormously challenging because there are a mind-boggling number of ways in which the same protein could theoretically fold to take on a 3D structure, according to a statement from DeepMind.

Twenty-five years ago, scientists created an international competition to compare various methods of predicting protein structure something of a "protein olympics," known as CASP, which stands for Critical Assessment of Protein Structure Prediction, according to The Guardian.

In this year's challenge, AlphaFold's performance was head and shoulders above its competitors'. It achieved a level of accuracy that researchers were not expecting to see for years.

"This computational work represents a stunning advance on the protein-folding problem, a 50-year-old grand challenge in biology," Venki Ramakrishnan, president of the Royal Society in the United Kingdom, who was not involved with the work, said in a statement. "It has occurred decades before many people in the field would have predicted. It will be exciting to see the many ways in which it will fundamentally change biological research."

For the competition, teams are given the amino acid sequences of about 100 proteins, the structures of which are known but have not been published, according to Nature News. The predictions are given a score from zero to 100, with 90 considered on par with the accuracy of experimental methods.

AlphaFold trained itself to recognize the relationship between the amino acid sequence and protein structure using existing databases. Then, it used a neural network a computer algorithm modeled on the way the human brain processes information to iteratively improve its prediction of the unpublished protein structures.

Overall, AlphaFold had a median score of 92.5. That's up from a score of less than 60 that the system achieved in its first CASP competition in 2018.

The system isn't perfect in particular, AlphaFold did not perform well in modeling groups of proteins that interact with each other, Nature News reported.

But the advance is a game-changer.

"I think it's fair to say this will be very disruptive to the protein-structure-prediction field. I suspect many will leave the field as the core problem has arguably been solved," Mohammed AlQuraishi, a computational biologist at Columbia University told Nature News. "It's a breakthrough of the first order, certainly one of the most significant scientific results of my lifetime."

DeepMind previously made headlines when it created an AI program, known as AlphaGo, that beat humans at the ancient game of Go.

Researchers hope AlphaFold can have many real-world applications. For example, it could help identify the structures of proteins involved in certain diseases and accelerate drug development.

DeepMind is currently working on a peer-reviewed paper on its work on AlphaFold, the Times reported.

Originally published on Live Science.

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AI makes huge progress predicting how proteins fold one of biology’s greatest challenges promising rapid drug development – The Conversation US

Takeaways

A deep learning software program from Google-owned lab DeepMind showed great progress in solving one of biologys greatest challenges understanding protein folding.

Protein folding is the process by which a protein takes its shape from a string of building blocks to its final three-dimensional structure, which determines its function.

By better predicting how proteins take their structure, or fold, scientists can more quickly develop drugs that, for example, block the action of crucial viral proteins.

Solving what biologists call the protein-folding problem is a big deal. Proteins are the workhorses of cells and are present in all living organisms. They are made up of long chains of amino acids and are vital for the structure of cells and communication between them as well as regulating all of the chemistry in the body.

This week, the Google-owned artificial intelligence company DeepMind demonstrated a deep-learning program called AlphaFold2, which experts are calling a breakthrough toward solving the grand challenge of protein folding.

Proteins are long chains of amino acids linked together like beads on a string. But for a protein to do its job in the cell, it must fold a process of twisting and bending that transforms the molecule into a complex three-dimensional structure that can interact with its target in the cell. If the folding is disrupted, then the protein wont form the correct shape and it wont be able to perform its job inside the body. This can lead to disease as is the case in a common disease like Alzheimers, and rare ones like cystic fibrosis.

Deep learning is a computational technique that uses the often hidden information contained in vast datasets to solve questions of interest. Its been used widely in fields such as games, speech and voice recognition, autonomous cars, science and medicine.

I believe that tools like AlphaFold2 will help scientists to design new types of proteins, ones that may, for example, help break down plastics and fight future viral pandemics and disease.

I am a computational chemist and author of the book The State of Science. My students and I study the structure and properties of fluorescent proteins using protein-folding computer programs based on classical physics.

After decades of study by thousands of research groups, these protein-folding prediction programs are very good at calculating structural changes that occur when we make small alterations to known molecules.

But they havent adequately managed to predict how proteins fold from scratch. Before deep learning came along, the protein-folding problem seemed impossibly hard, and it seemed poised to frustrate computational chemists for many decades to come.

The sequence of the amino acids which is encoded in DNA defines the proteins 3D shape. The shape determines its function. If the structure of the protein changes, it is unable to perform its function. Correctly predicting protein folds based on the amino acid sequence could revolutionize drug design, and explain the causes of new and old diseases.

All proteins with the same sequence of amino acid building blocks fold into the same three-dimensional form, which optimizes the interactions between the amino acids. They do this within milliseconds, although they have an astronomical number of possible configurations available to them about 10 to the power of 300. This massive number is what makes it hard to predict how a protein folds even when scientists know the full sequence of amino acids that go into making it. Previously predicting the structure of protein from the amino acid sequence was impossible. Protein structures were experimentally determined, a time-consuming and expensive endeavor.

Once researchers can better predict how proteins fold, theyll be able to better understand how cells function and how misfolded proteins cause disease. Better protein prediction tools will also help us design drugs that can target a particular topological region of a protein where chemical reactions take place.

The success of DeepMinds protein-folding prediction program, called AlphaFold, is not unexpected. Other deep-learning programs written by DeepMind have demolished the worlds best chess, Go and poker players.

In 2016 Stockfish-8, an open-source chess engine, was the worlds computer chess champion. It evaluated 70 million chess positions per second and had centuries of accumulated human chess strategies and decades of computer experience to draw upon. It played efficiently and brutally, mercilessly beating all its human challengers without an ounce of finesse. Enter deep learning.

On Dec. 7, 2017, Googles deep-learning chess program AlphaZero thrashed Stockfish-8. The chess engines played 100 games, with AlphaZero winning 28 and tying 72. It didnt lose a single game. AlphaZero did only 80,000 calculations per second, as opposed to Stockfish-8s 70 million calculations, and it took just four hours to learn chess from scratch by playing against itself a few million times and optimizing its neural networks as it learned from its experience.

AlphaZero didnt learn anything from humans or chess games played by humans. It taught itself and, in the process, derived strategies never seen before. In a commentary in Science magazine, former world chess champion Garry Kasparov wrote that by learning from playing itself, AlphaZero developed strategies that reflect the truth of chess rather than reflecting the priorities and prejudices of the programmers. Its the embodiment of the clich work smarter, not harder.

Every two years, the worlds top computational chemists test the abilities of their programs to predict the folding of proteins and compete in the Critical Assessment of Structure Prediction (CASP) competition.

In the competition, teams are given the linear sequence of amino acids for about 100 proteins for which the 3D shape is known but hasnt yet been published; they then have to compute how these sequences would fold. In 2018 AlphaFold, the deep-learning rookie at the competition, beat all the traditional programs but barely.

Two years later, on Monday, it was announced that Alphafold2 had won the 2020 competition by a healthy margin. It whipped its competitors, and its predictions were comparable to the existing experimental results determined through gold standard techniques like X-ray diffraction crystallography and cryo-electron microscopy. Soon I expect AlphaFold2 and its progeny will be the methods of choice to determine protein structures before resorting to experimental techniques that require painstaking, laborious work on expensive instrumentation.

One of the reasons for AlphaFold2s success is that it could use the Protein Database, which has over 170,000 experimentally determined 3D structures, to train itself to calculate the correctly folded structures of proteins.

The potential impact of AlphaFold can be appreciated if one compares the number of all published protein structures approximately 170,000 with the 180 million DNA and protein sequences deposited in the Universal Protein Database. AlphaFold will help us sort through treasure troves of DNA sequences hunting for new proteins with unique structures and functions.

As with the chess and Go programs AlphaZero and AlphaGo we dont exactly know what the AlphaFold2 algorithm is doing and why it uses certain correlations, but we do know that it works.

Besides helping us predict the structures of important proteins, understanding AlphaFolds thinking will also help us gain new insights into the mechanism of protein folding.

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One of the most common fears expressed about AI is that it will lead to large-scale unemployment. AlphaFold still has a significant way to go before it can consistently and successfully predict protein folding.

However, once it has matured and the program can simulate protein folding, computational chemists will be integrally involved in improving the programs, trying to understand the underlying correlations used, and applying the program to solve important problems such as the protein misfolding associated with many diseases such as Alzheimers, Parkinsons, cystic fibrosis and Huntingtons disease.

AlphaFold and its offspring will certainly change the way computational chemists work, but it wont make them redundant. Other areas wont be as fortunate. In the past robots were able to replace humans doing manual labor; with AI, our cognitive skills are also being challenged.

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Genesis Therapeutics raises $52M A round for its AI-focused drug discovery mission – TechCrunch

Sifting through the trillions of molecules out there that might have powerful medicinal effects is a daunting task, but the solution biotech has found is to work smarter, not harder. Genesis Therapeutics has a new simulation approach and cross-disciplinary team that has clearly made an impression: the company just raised a $52 million A round.

Genesis competed in the Startup Battlefield at Disrupt last year, impressing judges with its potential, and obviously others saw it as well in particular Rock Springs Capital, which led the round.

Over the last few years many companies have been formed in the drug discovery space, powered by increased computing and simulation power that lets them determine the potential of molecules in treating certain diseases. At least thats the theory. The reality is a bit messier, and while these companies can narrow the search, they cant just say here, a cure for Parkinsons.

Founder Evan Feinberg got into the field when an illness he inherited made traditional lab work, as an intern at a big pharma company, difficult for him. The computational side of the field, however, was more accessible and ended up absorbing him entirely.

He had dabbled in the area before and arrived at what he feels is a breakthrough in how molecules are represented digitally. Machine learning has, of course, accelerated work in many fields, biochemistry among them, but he felt that the potential of the technology had not been tapped.

I think initially the attempts were to kind of cut and paste deep learning techniques, and represent molecules a lot like images, and classify them like youd say, this is a cat picture or this is not a cat picture, he explained in an interview. We represent the molecules more naturally: as graphs. A set of nodes or vertices, those are atoms, and things that connect them, those are bonds. But were representing them not just as bond or no bond, but with multiple contact types between atoms, spatial distances, more complex features.

The resulting representation is richer and more complex, a more complete picture of a molecule than youd get from its chemical formula or a stick diagram showing the different structures and bonds. Because in the world of biochemistry, nothing is as simple as a diagram. Every molecule exists as a complicated, shifting 3D shape or conformation where important aspects like the distance between two carbon formations or bonding sites is subject to many factors. Genesis attempts to model as many of those factors as it can.

Step one is the representation, he said, but the logical next step is, how does one leverage that representation to learn a function that takes an input and outputs a number, like binding affinity or solubility, or a vector that predicts multiple properties at once?

Thats the work theyve focused on as a company not just creating a better model molecule, but being able to put a theoretical molecule into simulation and say, it will do this, it wont do this, it has this quality but not that one.

Some of this work may be done in partnerships, such as the one Genesis has struck up with Genentech, but the teams could very well find drug candidates independent of those, and for that reason the company is also establishing an internal development process.

The $52 million infusion ought to do a lot to push that forward, Feinberg wrote in an email:

These funds allow us to execute on a number of critical objectives, most importantly further pioneering AI technologies for drug development and advancing our therapeutics pipeline. We will be hiring more top notch AI researchers, software engineers, medicinal chemists and biotech talent, as well as building our own research labs.

Other companies are doing simulations as well and barking up the same tree, but Feinberg says Genesis has at least two legs up on them, despite the competition raising hundreds of millions and existing for years.

Were the only company in the space thats working at the intersection of modern deep neural network approaches and biophysical simulation conformational change of ligands and proteins, he said. And were bringing this super technical platform to experts who have taken FDA-approved drugs to market. Weve seen tremendous value creation just from that the chemists inform the AI too.

The recent breakthrough of AlphaFold, which is performing the complex task of simulation protein folding far faster than any previous system, is as exciting to Feinberg as to everyone else in the field.

As scientists, we are incredibly excited by recent progress in protein structure prediction. It is an important basic science advance that will ultimately have important downstream benefits to the development of novel therapeutics, he wrote. Since our Dynamic PotentialNet technology is unique in how it leverages 3D structural information of proteins, computational protein folding similar to recent progress in cryo-EM is a nice complementary tailwind for the Genesis AI Platform. We applaud all efforts to make protein structure more accessible such that therapeutics can be more easily developed for patients of all conditions.

Also participating in the funding round were T. Rowe Price Associates, Andreessen Horowitz (who led the seed round), Menlo Ventures and Radical Ventures.

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