Under the Surface Podcast

Shannon's Entropy and the Quest for Peptide Representation

Check out the next episode of our podcast, Under the Surface. In episode 19, Shannon's Entropy and the Quest for Peptide Representation, we report live from a speakeasy with Shannon Smith, Genentech postdoc, on how she went from a pre-med background to studying computational structural biology under Jerome Baudry at the University of Tennessee, graduating with a PhD from Jens Meiler at Vanderbilt, and coming to Genentech. They get right into it with topics such as the difficulties of small molecule docking, the elegance of mathematical approaches, the absolute requirement for developing a novel geometric language for describing macrocyclic peptides (hairpins and hair ties, anyone?), the human element of research, life in the industry vs academia, too much technology distracting us from thinking and even the dream of becoming a National Geographic photographer. This episode was recorded at our 2026 UGM in Montreal. Timecodes: (04:30) Shannon shares her undergraduate path at Ohio State and how discovering computational structural biology under Jerome Baudry changed her trajectory . (10:15) Shannon describes her "aha!" moment watching her first docking simulation in MOE. (19:00) The differences between industry and academia. (34:15) Shannon introduces her pet project on macrocyclic peptides and why current descriptors fall short without a new geometric vocabulary . (42:00) Shannon's secret dream of becoming a National Geographic photographer. Listener discretion is advised.

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The FoF (Filet-O-Fish) Turning Point to OpenFF (Open Force Field)

Listen to the next episode of our podcast, Under the Surface. In episode 18, The FoF (Filet-O-Fish) Turning Point to OpenFF (Open Force Field), we chat with @Lily Wang, Science Lead at the Open Force Field Initiative (@OpenFF), about the unexpected, very human moment that set her on the path to computational chemistry — a cold Filet‑O‑Fish eaten at 1 a.m. after a disastrous night in the lab. Lily shares that she first wanted to study art. Still, a close friend's lupus diagnosis inspired her to choose science instead, leading to advancements in molecular simulation and force fields that benefit computational chemistry research. We also cover recent advances in molecular modeling, such as neural-network-based charge models and improved protein force fields, to excite researchers about future innovations. Topics: Lily's path from the arts to computational chemistry What OpenFF and OMSF actually do Building more advanced force fields Sage 2.3 and neural‑network charge models Expanding force fields for proteins and nucleic acids Funding open science and partnering with industry Listener discretion is advised. Timestamps: (02:27) What is OpenFF? (04:10) How to make models more accurate. (05:42) What made her want to be a scientist in the first place. (07:37) The moment she realized working with computers in chemistry was perfect for her. (15:42) How scientists use computers to study the outside of cells. (20:22) The difference between super-detailed and simpler computer models scientists use to study chemistry. (26:23) How sharing science models helps people in schools and company teams to make faster progress. (35:03) How scientists can share what they learn without giving away anyone's secrets. (46:18) What's new in Sage 2.3? (52:05) Why it's tricky to model electricity in molecules, and where scientists are going next with this research. (54:45) Two ways scientists build their models. (58:45) Looking ahead: Quantum mechanics and AI could change how scientists work in the future. (01:08:15) The Deschenes Dilemma: Lily shares what she might do if she weren't a scientist. Resources & Links: Open Force Field Initiative 2.3 Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model OpenFF GitHub Repository OpenMSF (Open Molecular Software Foundation) Connect with Lily Wang: LinkedIn

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Building Collaborative Drug Discovery Tools with Barry Bunin

*Content Warning: This episode includes discussions of trauma, loss, and near‑death experiences. Please take care while listening, and reach out to a mental health professional or someone you trust if these topics become overwhelming.* Listen to the next episode of our podcast, Under the Surface. In episode 17, Building Collaborative Drug Discovery Tools, we feature an in-depth interview with Barry Bunin, CEO of Collaborative Drug Discovery, about his journey from chemist to entrepreneur. He shares how his background and desire to make a difference have shaped his company's mission and technology. Here's what we discuss: Barry Bunin's background and what inspired his purpose How CDD started and became a leader in sharing science safely Why CDD Vault was built to keep research private, secure, and easy to use How teamwork and sharing data make drug discovery faster Finding the right balance between sharing and privacy How new tech like AI helps scientists work together Caring about people, having an impact, and doing good in science Barry's book shows the power of working together and being creative This episode brings together science, entrepreneurship, and the personal stories that inspire innovation. Listener discretion is advised. TIMESTAMPS: (03:00) Barry talks about starting out in science, wanting to make a difference, and how that shaped his work. (06:00) How Barry's personal experiences led to his book and his current journey. (06:33) Content Warning begins. (07:10) Content Warning ends. (10:00) Mixing hands-on chemistry with computer tools to get better results. (15:00) How Barry got interested in combining chemistry and technology early on. (20:00) Moving from lab work to starting software companies. (25:00) What CDD stands for: their values, company culture, and mission. (30:00) Working together in drug discovery, and how to keep things open but private. (33:24) Content Warning begins. (37:33) Content Warning ends. (35:00) Real stories from the field, and why being human matters in science. (40:00) Keeping data safe and models using tech like federated learning. (50:00) How Barry's book came together. (1:00:00) Looking ahead: AI, collaboration tools, and making a positive impact. (1:06:40) The "Deschenes Dilemma": What happens if you can't stop doing science? (1:08:00) Thinking about legacy, inspiring future generations, and making your mark. Resources & Links: Inside CDD Vault — A Different Kind of Silicon Valley Success Story: Behind the Code: The Human Side of Collaborative Drug Discovery (on Amazon) Collaborative Drug Discovery (CDD) The Human Side of Collaborative Drug Discovery How Do B2B Companies Hold Onto Their Purpose as They Grow? Connect with Barry Bunin: LinkedIn

When Proteins Move: Woody Sherman on Computational Chemistry, Molecular Simulation, and the Future of AI in Drug Discovery

Check out the next episode of our podcast, Under the Surface. In episode 16, When Proteins Move: Woody Sherman on Computational Chemistry, Molecular Simulation, and the Future of AI in Drug Discovery, we chat with Woody Sherman, Founder and Chief Innovation Officer at PsiThera, and a longtime leader in computational chemistry, about how he went from studying quantum polymers to shaping modern tools like Induced Fit Docking. Woody shares the moment that pulled him into protein simulations, his early exposure to AI at MIT, and how an internship at Biogen set him on the path to industry. He also reflects on his years at Schrödinger, building solutions, writing code, and learning how to solve real problems for scientists. Topics: How application scientists help connect research with real-world industry needs Woody's journey from university research to starting Silicon Therapeutics How tools like induced fit docking were created How drug discovery platforms have changed over time What's different between working in industry and in academia What's next for open molecular software and AI working together (02:05) Why mentorship matters for scientists (04:15) Woody's path through school and research (09:10) Shifting into custom molecular simulations (12:00) Going from the academic world to industry (15:00) Creating new tools for drug discovery at Schrodinger (22:10) Putting together a team of experts (26:15) Working together on drug design platforms (34:00) Leading application science teams around the world (41:45) Starting up Silicon Therapeutics (45:58) Progress in the development of the STING agonist medicine (49:00) Launching PsiThera (56:30) Focusing on inflammation and the immune system (60:15) Sharing science and data openly (69:00) How AI will shape the future of drug discovery (80:30) What Woody enjoys outside of work (82:20) Final thoughts and getting involved with the community Listener discretion is advised.

Fells' Elements of Success: A Periodic Journey

Check out the next episode of our podcast, Under the Surface! In episode 15, Fells' Elements of Success: A Periodic Journey, we immerse ourselves in the world of chemistry and career alchemy with James Fells. From his early days as a curious freshman to his role as an Associate Director, In Silico Discovery at Johnson & Johnson Innovative Medicine, James recounts his journey through the ups and downs of the scientific realm and the importance of guidance along the way. Hear how his childhood curiosity about Gargamel inspired his success, how he moved between academia and industry, and why his story stands out. We think this episode will really connect with you. Listener discretion is advised. (02:12) The story behind the early use of MOE software in 1999 (03:36) Childhood obsession with potions and how it sparks real science (07:00) Funding, scholarships, and the importance of independence (08:41) Making the leap from academia to industry: speed and culture shock (12:33) The value of humility, openness, and collaboration in pharma (16:15) Crafting winning fellowship applications and proactive networking (20:19) Transitioning from postdoc to industry: timing and strategy (24:17) How industry teams differ from academia in hierarchy and respect (37:33) The big cultural shifts moving from Merck to Johnson & Johnson (45:18) The importance of company culture, openness, and shared lessons learned (49:12) J&J's evolving approach to science, leadership, and opportunity (57:47) Reflections: What he'd do differently, advice for future scientists (62:03) If not in science, what would James do? Coach? Math teacher? (63:53) Final thoughts: Exploring opportunities, being adaptable, and following your curiosity Subscribe & listen to all episodes of our podcast: https://sites.libsyn.com/459216/underthesurface Follow us on LinkedIn & X

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SVL: Santavy vs Labute - The HoliDAVE Edition

Welcome to the last episode of 2025 for our podcast, Under the Surface! In this episode, SVL: Santavy vs Labute - The HoliDAVE Edition, get cozy with this special holiday edition of "Under the Surface"! Chris Williams and Dave Thompson are here to share laughs, swap stories, and spread some cheer as they chat with CCG's always-jolly Principal Scientist, Martin Santavy. From the wild beginnings of programming to the everyday adventures of debugging, this episode takes you on a fun-filled ride through the world of computational chemistry. There's plenty of laughter, a sprinkle of science magic, and a whole lot of heart as we talk about the quirks of coding and the power of good communication. Whether you're a science fan or just love a great story, come join us—grab your favorite mug, settle in, and let's celebrate the season together! Listener discretion is advised. 03:45 The Journey to CCG: Early Days and Influences 10:02 The Development of SVL: A New Programming Language 14:56 Challenges and Innovations in Computational Chemistry 20:55 The Evolution of CCG and Its Market Position 22:23 Reflections on Missed Opportunities 24:25 The Evolution of Software in Chemistry 26:50 Navigating the Language of Chemistry 30:54 The Importance of Communication in Science 35:32 Debugging and Problem Solving 42:45 The Joy of Software Development 50:35 Passion for Science and Software Subscribe & listen to all episodes of our podcast: https://sites.libsyn.com/459216/underthesurface Follow us on LinkedIn & X

Unfiltered Leadership with Erin Davis

In episode 13, Unfiltered Leadership, we dive into the fascinating journey of Erin Davis, who proves that the path to becoming a CTO at X-Chem is paved with caffeine, coding, and a touch of chaos. Erin's story is a masterclass in creativity and resilience. Tune in for tales of tech debt, DNA-encoded libraries (DELs), questioning authority, and why she believes humans are just 'meat sacks' trying to make sense of it all. This episode is a delightful mix of humor, inspiration, perfect for anyone who loves a good science story with a side of laughter. This episode will leave you inspired and entertained! Listener discretion is advised. Subscribe & listen to all episodes of our podcast: https://bit.ly/3WQGPKY Follow us on LinkedIn & X

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Never Mind the Woman Behind the Curtain with Dr. Sarah Witzke

In episode 12, Never Mind the Woman Behind the Curtain, we welcome Dr. Sarah Witzke, Senior Application Scientist at CCG, who spills the beans on the not-so-secret life of support scientists in drug discovery. Think of it as a behind-the-scenes tour as to why you shouldn't ignore the people behind the curtain. Sarah shares her multifaceted journey, hopping from academia to the industry, kind of like a superhero changing outfits—except her cape was probably a lab coat. She unpacks the art of juggling her responsibilities and her knack for customer interaction. Spoiler alert: building trust with clients is crucial, unless you want them to think you're just some mad scientist in a basement! They explore how remote work has flipped team communication on its head. You might think it's just a lot of Zoom calls and pajama pants, but there's more to it. Sarah reflects on her career path, her growth, and the ups and downs with impostor syndrome along the way. And to top it all off, she dishes out some golden advice for aspiring application scientists — hint: humility and adaptability are your BFFs. So, grab a snack and settle in for a fun and insightful chat that might just inspire you to embrace your inner scientist — or perhaps become one.

Crystal Clear: Unveiling the Secrets of Crystallography and Drug Design

In our next episode, we're joined by Jason Cole, a Senior Research Fellow at the Cambridge Crystallographic Data Center (CCDC). He shares his fascinating journey, starting from his childhood in Italy, where his love for science blossomed, all the way to his impressive career in computational chemistry and crystallography. We chat about what CCDC does in terms of gathering and sharing crystallographic data, the ups and downs of software development in this field, and why it's so crucial to validate docking software. Jason also highlights the importance of data standards, the philanthropic mission of CCDC, and what the future holds for drug discovery, particularly with the exciting possibilities of artificial intelligence (AI) and quantum computing. It's a great conversation packed with insights!

The Passport to Knowledge and Discovery with Fernando Garces

In our first episode of 2025, our hosts, Chris Williams and Dave Thompson, have the pleasure of speaking to Fernando Garces, CEO and co-founder of BioGlyph. Leading us from the sunny climes of Portugal through the tropical paradise that is London, on route to the West Coast of the US and A, Fernando shares his evolving love of science through the heights of academia, into industry, and now as CEO of a software company he co-founded to improve the modeling of complex multispecifics. Important questions are unpacked throughout - is London really a tropical paradise? How long can we keep milking podcast episode titles that take advantage of the homophonic property of pharma and farm? Oh, and we have another surprising guest answer to the 'Deschênes Dilemma'… It is not to quote G. K. Chesterton, a proper nailbiter!

Rebecca Swett on The Power of Automation in Drug Development

In our final episode of 2024, host Chris Williams and guest co-host, Under the Surface Executive Producer and CCG Vice President, Alain Deschênes have a long overdue chat with computational drug discovery rock star Rebecca Swett. Rebecca shares her journey from her academic beginnings to her current role at X-Chem, via roles at Novartis, Vertex, and Relay. Rebecca's wide-ranging experience shines through as the conversation wends its way through cutting-edge computational chemistry covering machine learning, molecular dynamics, and DNA-encoded libraries. At the scale Rebecca works at, automation is key, so this topic comes up too. We're not going to lie; it's a lot. And, of course, there's more … Rebecca highlights the significance of allyship and representation for women in science, and the role of community (with a shout-out to the long-running BAGIM modeling forum). Also, in the inaugural asking of the 'Deschênes Dilemma,' we find out what Rebecca would be doing if she wasn't doing all of the above …

The Molecular Assassin Dr. Arijit Basu

On episode 8 of Under the Surface, we're joined by The Molecular Assassin, Arijit Basu. Arijit describes his journey from India to the US via a transformative sabbatical in Israel. Landing in the Langer lab at MIT and then finding his industrial legs, Arijit turns to computational toxicology as a way to ensure that drug hunters enable the concept of Safety by Design as a core tenant for how they're navigating chemical space. He doesn't discuss how he got his cool nickname though, so if that's what you're after, you will be out of luck. This episode was recorded live in Montreal at our 2024 UGM.

On Being The First [Second?] with Eric Larson

This next episode of Under the Surface has us speaking to crystallographer Eric Larson. In episode 7, as you'll hear, Eric's a little nervous about having his thoughts committed to 'perpetuity.' But, as you'll also hear, he does a great job. As our first second structural biologist on the show, he tells us about how he got into the field, the very real logistical challenges of working in industry, and his evocative description of what it feels like to peek 'behind the veil' and be the first on the planet to observe the structure of a previously unknown protein. It's a magical episode This episode was recorded live in Montreal at our 2024 UGM.

Revolutionizing Nanoscale Visualization

Check out the next episode of our podcast, Under the Surface! In episode 6, Revolutionizing Nanoscale Visualization, we talk to Nanome CEO and co-founder Steve McCloskey. In a virtual rollercoaster of a conversation, he shares Nanome's scrappy beginnings, the challenge and excitement of bringing new ways of interacting with models to the science community, and paints a vivid picture of an exciting element of the future of molecular modeling. It's Reality Jim, but not as we know it… Interested in giving this a test drive? Contact hello@nanome.ai to set up a demo with Nanome.

Farm to Pharma with Dr. Dan McKay

In episode 5, Farm to Pharma, we talk to Dr. Dan McKay about his career in the pharmaceutical industry (he grew up on a Farm! See what we did there … ?). As a pioneer in the applied use of quantum mechanics, Dan describes his break into the industry from academia, his realization of the critical importance of water in understanding 'what's going on', and offers some pointed observations on the applicability of artificial intelligence and machine learning in drug discovery. Throughout our time with him, Dan's stories paint a vivid and exciting picture of what it means to support a modern discovery effort. Also, in a first for Under the Surface, we ask something of you, our audience. Can you help us, help Dan?

A CHRIStmas Carol: A Super Special HoliDAVE Edition

Welcome to the last episode of the year for our podcast, Under the Surface! In this episode, A CHRIStmas Carol, we conjure up some jovial spirits of the past as our Super Senior co-host Dave grills his colleagues on the founding, early years, and development of the Chemical Computing Group. As you'll hear, Dave manages to make Research Group Leader, Anna Lin, and his regular co-host, Chris Williams, feel deeply uncomfortable and encourages them to step out of their inherent Canadian humility and embrace the fact that they contributed to the building of a thing that is still going strong - 30 years on! Reminiscences are shared, the field is reflected upon, and famous Canadians are listed. It is, dear listener, a roller coaster of an emotional ride.

Instructions for a Life in Science with Dr. Vanita Sood

In episode 3, Instructions for a Life in Science, we talk to Dr. Vanita Sood about her experiences as a drug hunter. Vanita candidly shares her career journey, reflecting back on the choices she made, the opportunities and challenges she navigated, and the transformational science she drove. She describes her recent transition from a large pharma company to a startup environment and the critical considerations she's had to deal with. Throughout we talk about AI in discovery, the science of serendipity, and Mary Oliver the naturist and poet. Vanita expounds the spirit of paying attention, being astonished, and sharing this enthusiasm with others.. Strap in folks. Takeaways: Dr. Vanita Sood has 15 years of experience in drug discovery. AI in drug discovery has shifted from skepticism to enthusiasm. Switching fields can provide new perspectives and opportunities. Drug discovery requires teamwork and collaboration. Building connections in academia can lead to industry opportunities. The patient-centric approach drives drug discovery priorities. Data generation for AI needs to be consistent and relevant. Human insight is essential for interpreting complex biological data. Exploring new chemical spaces is crucial for innovation. Serendipity can lead to unexpected breakthroughs in research. Relying on machine learning for drug discovery raises concerns about data complexity. The best drug discoveries often come from unexpected patterns in data. Documentation in pharma is generally better than in academia, but still has gaps. Machine learning models need interpretability to ensure reliability and understanding. Transitioning from a large pharma environment to a startup presents unique learning opportunities. Collaboration in the pharma industry fosters a collegial environment despite competitive pressures. Terminated projects can provide valuable data for machine learning models. Attention to detail is crucial in scientific discovery and data curation. Balancing deep expertise with a general understanding of other disciplines is essential in drug discovery. AI and machine learning are transforming the landscape of drug discovery, requiring new skill sets.

Fun with Pharmacophores

Check out the next episode of our podcast, Under the Surface! In episode 2, Fun with Pharmacophores, we talk to Dr. Scott Rowland about pharmacophore-based techniques and their role in understanding receptor–ligand interactions, and ultimately, how they contribute to the design of new drugs. Recently retired, following decades in the pharmaceutical industry, Scott tells us about his journey through the field and his deep appreciation for collaborative science. Scott hasn't completely hung up his abacus just yet though, and he tells us about his recent consultative adventures too! How have we managed to fit all of this in one episode? It's a mystery. Takeaways: Dr. Scott Rowland has over 20 years of experience in drug discovery. Structure-based drug design is now widely accepted but still has untapped potential. Collaboration between medicinal chemists and computational chemists is crucial for success. 3D structures provide valuable insights for drug design. Team dynamics play a significant role in the drug discovery process. Consulting allows for flexibility and creativity in biotech startups. Pharmacophores are essential for understanding drug interactions. The concept of pharmacophores is evolving and is not static. Pharmacophore efficiency could be a new metric in drug design. The future of drug discovery relies on collaboration and innovative thinking.

Computers to Find Big Molecules with Dr. Sandeep Kumar

In episode 1 of our yet-to-win award podcast, we talk to Dr. Sandeep Kumar, Distinguished Research Fellow in Biotherapeutics at Boehringer Ingelheim about how he uses computers to help develop and deliver biopharmaceuticals and his thoughts on the increasing importance of computational methods in drug discovery. It gets controversial at times, so, you know, just a warning on that. See more: Computational Antibody Discovery: State of the Art: https://www.antibodysociety.org/computational-antibody-discovery-state-of-the-art/ Takeaways: Dr. Sandeep Kumar is driven by a desire to help patients. Computational methods can revolutionize antibody discovery. In silico antibody discovery can overcome traditional limitations. AI can generate vast libraries of antibodies efficiently. Medicine-like profiles can improve drug developability. Collaboration between tech and biotech is essential. Digital transformation is crucial for the pharmaceutical industry. Data digitization is necessary for effective informatics systems. Computational predictions need to be validated in the lab. The future of drug discovery lies in integrating computation with experimentation.

Introducing Under the Surface with Chemical Computing Group

What's this all about, you ask? In today's inaugural episode of our sure-to-be award-winning podcast, we'll cover the who, what, and why we decided to create this podcast. As well as preview industry topics we'll be covering in future episodes. This is not your average science podcast - Welcome to Under the Surface. For more information on Chemical Computing Group, head to: https://www.chemcomp.com/. The podcast aims to share: Insights from the field of drug discovery. Computational chemistry is evolving with new technologies and AI. There is a mix of hope and skepticism in the field. Understanding the sociology behind software use is important. Big pharma and small biotech have different approaches to innovation. The history of CCG provides valuable context for current practices. Structural information plays a crucial role in drug discovery. The podcast will feature discussions with industry experts. New technologies are often applied in innovative ways by smaller firms. The future of drug discovery is promising with advancements in AI.

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