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Under the Surface Podcast: Daily Summaries Delivered
by CCG | Chemical Computing Group Podcast
Under the Surface is Chemical Computing Group's podcast where science meets storytelling in the world of computer‑aided drug discovery. Each episode brings you inside the breakthroughs shaping modern computational chemistry — from molecular modeling and AI‑powered design to the personal journeys of the researchers driving innovation forward. Join pioneering scientists, industry leaders, and curious minds as we explore how in silico techniques accelerate discovery, transform workflows, and reveal the human side of scientific progress.
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- 1 weeks ago1h 3m
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: Shannon shares her undergraduate path at Ohio State and how discovering computational structural biology under Jerome Baudry changed her trajectory . Shannon describes her "aha!" moment watching her first docking simulation in MOE. The differences between industry and academia. Shannon introduces her pet project on macrocyclic peptides and why current descriptors fall short without a new geometric vocabulary . Shannon's secret dream of becoming a National Geographic photographer. Listener discretion is advised.
- Sep 29, 20261h 9m
The FoF (Filet-O-Fish) Turning Point to OFF (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 OFF (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: What is OpenFF? How to make models more accurate. What made her want to be a scientist in the first place. The moment she realized working with computers in chemistry was perfect for her. How scientists use computers to study the outside of cells. The difference between super-detailed and simpler computer models scientists use to study chemistry. How sharing science models helps people in schools and company teams to make faster progress. How scientists can share what they learn without giving away anyone's secrets. What's new in Sage 2.3? Why it's tricky to model electricity in molecules, and where scientists are going next with this research. Two ways scientists build their models. Looking ahead: Quantum mechanics and AI could change how scientists work in the future. 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 <a href= "https://omsf.io/programs/projects/ope
- Aug 4, 20261h 4m
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: - Barry talks about starting out in science, wanting to make a difference, and how that shaped his work. - How Barry's personal experiences led to his book and his current journey. - Mixing hands-on chemistry with computer tools to get better results. - How Barry got interested in combining chemistry and technology early on. - Moving from lab work to starting software companies. - What CDD stands for: their values, company culture, and mission. - Working together in drug discovery, and how to keep things open but private. - Real stories from the field, and why being human matters in science. - Keeping data safe and models using tech like federated learning. - How Barry's book came together. - Looking ahead: AI, collaboration tools, and making a positive impact. - The "Deschenes Dilemma": What happens if you can't stop doing science? - Thinking about legacy, inspiring future generations, and making your mark. <p
- Jun 16, 20261h 22m
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 and the Birth of Induced Fit Docking, we chat with Woody Sherman, Chief Scientist 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 Why mentorship matters for scientists Woody's path through school and research Shifting into custom molecular simulations Going from the academic world to industry Creating new tools for drug discovery at Schrodinger Putting together a team of experts Working together on drug design platforms Leading application science teams around the world Starting up Silicon Therapeutics Progress in the development of the STING agonist medicine Launching PsiThera Focusing on inflammation and the immune system Sharing science and data openly How AI will shape the future of drug discovery What Woody enjoys outside of work Final thoughts and getting involved with the community Listener discretion is advised.
- Mar 31, 20261h 6m
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
- Dec 22, 202552 min
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
- Nov 18, 20251h 15m
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
- Aug 26, 202546 min
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.
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About Under the Surface Podcast
Under the Surface is Chemical Computing Group's podcast where science meets storytelling in the world of computer‑aided drug discovery. Each episode brings you inside the breakthroughs shaping modern computational chemistry — from molecular modeling and AI‑powered design to the personal journeys of the researchers driving innovation forward. Join pioneering scientists, industry leaders, and curious minds as we explore how in silico techniques accelerate discovery, transform workflows, and reveal the human side of scientific progress.
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