A primer on molecular dynamics - by Abhishaike Mahajan

7.8k words, 36 minutes reading time

Introduction How does MD work in practice? System Definition Force Fields The basic definition The details Energy minimization + equilibration Production simulation Interesting miscellaneous things Bypassing small timescales Quantum effects Free energy calculations Case studies Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2 Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin Conclusion I’ve recently become very interested in molecular dynamics, or MD. Why…

related reading

• A primer on molecular dynamicsowlposting.com
• Protein World Model | Biohubbiohub.ai
• AlphaFold2 @ CASP14: “It feels like one’s child has left home.” << Some Thoughts on a Mysterious Universemoalquraishi.wordpress.com
• The Illustrated AlphaFold | Elana Simonelanapearl.github.io
• Quantum Chemistry in Drug Discovery | Rowanrowansci.com
• Can AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1)owlposting.com
• diffuse.onediffuse.one
• Multiscale Ensemble Modeling of Intrinsically Disordered Proteins: p53 N-Terminal Domain - PMCncbi.nlm.nih.gov
• Biology is a Burrito (& Other Essays)burrito.bio
• One-shot design of functional protein binders with BindCraftnature.com
• Quantum Chemistry in Drug Discoveryrowansci.substack.com
• Ludovico Comitoludocomito.dev