Explore every episode of the podcast AI in Biomolecules

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:58 - Joint Geometric-Chemical Distance for Protein Surfaces https://export.arxiv.org/pdf/2603.09860.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:55 - Adversarial Domain Adaptation Enables Knowledge Transfer Across Heterogeneous RNA-Seq Datasets https://export.arxiv.org/pdf/2603.08062.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 1:04 - Sampling-based Continuous Optimization for Messenger RNA Design https://export.arxiv.org/pdf/2603.06559.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:41 - Inference-Time Toxicity Mitigation in Protein Language Models https://export.arxiv.org/pdf/2603.04045.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:52 - ProtRLSearch: A Multi-Round Multimodal Protein Search Agent with Large Language Models Trained via Reinforcement Learning https://export.arxiv.org/pdf/2603.01464.pdf 4:54 - Multimodal Mixture-of-Experts with Retrieval Augmentation for Protein Active Site Identification https://export.arxiv.org/pdf/2603.01511.pdf 9:44 - Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles https://export.arxiv.org/pdf/2603.02406.pdf 13:09 - Deep learning-guided evolutionary optimization for protein design https://export.arxiv.org/pdf/2603.02753.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:42 - Inference-time optimization for experiment-grounded protein ensemble generation https://export.arxiv.org/pdf/2602.24007.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:56 - Induction Meets Biology: Mechanisms of Repeat Detection in Protein Language Models https://export.arxiv.org/pdf/2602.23179.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:50 - Spectral entropy of the discrete Hasimoto effective potential exposes sub-residue geometric transitions in protein secondary structure https://export.arxiv.org/pdf/2602.21787.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:47 - PIS: A Physics-Informed System for Accurate State Partitioning of $Aβ_{42}$ Protein Trajectories https://export.arxiv.org/pdf/2602.19444.pdf 4:45 - Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference https://export.arxiv.org/pdf/2602.20449.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:41 - Physical principles of building protein megacomplexes in a crowded milieu https://export.arxiv.org/pdf/2602.14005.pdf 4:54 - Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability https://export.arxiv.org/pdf/2602.14828.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:48 - Point transformer for protein structural heterogeneity analysis using CryoEM https://export.arxiv.org/pdf/2601.18713.pdf 5:29 - Structure-based RNA Design by Step-wise Optimization of Latent Diffusion Model https://export.arxiv.org/pdf/2601.19232.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 1:02 - Case-Guided Sequential Assay Planning in Drug Discovery https://export.arxiv.org/pdf/2601.14710.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:50 - Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics https://export.arxiv.org/pdf/2601.11012.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:59 - MMPG: MoE-based Adaptive Multi-Perspective Graph Fusion for Protein Representation Learning https://export.arxiv.org/pdf/2601.10157.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:49 - Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning https://arxiv.org/pdf/2601.05792.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 1:02 - Roadmap for Condensates in Cell Biology https://arxiv.org/pdf/2601.03677.pdf 6:17 - Investigating Knowledge Distillation Through Neural Networks for Protein Binding Affinity Prediction https://arxiv.org/pdf/2601.03704.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:00 - Paper (ID: 2601.00599) https://arxiv.org/abs/2601.00599 4:29 - Paper (ID: 2601.00618) https://arxiv.org/abs/2601.00618 8:28 - Paper (ID: 2601.00769) https://arxiv.org/abs/2601.00769 12:34 - Fold-switching proteins push the boundaries of conformational ensemble prediction https://arxiv.org/pdf/2601.01740.pdf 17:28 - Paper (ID: 2601.02265) https://arxiv.org/abs/2601.02265 ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:00 - Paper (ID: 2512.23784) https://arxiv.org/abs/2512.23784 4:20 - SeedProteo: Accurate De Novo All-Atom Design of Protein Binders https://arxiv.org/pdf/2512.24192.pdf 8:54 - SeedFold: Scaling Biomolecular Structure Prediction https://arxiv.org/pdf/2512.24354.pdf 13:39 - Paper (ID: 2512.24643) https://arxiv.org/abs/2512.24643 ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:00 - Clever Hans in Chemistry: Chemist Style Signals Confound Activity Prediction on Public Benchmarks https://arxiv.org/pdf/2512.20924.pdf ---------------------------------------- bibcast.com

This podcast is brought to you by bibcast. ---------------------------------------- Papers included in this episode: 0:00 - Methods for Analyzing RNA Pseudoknots via Chord Diagrams and Intersection Graphs https://arxiv.org/pdf/2512.19939.pdf 4:12 - MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing https://arxiv.org/pdf/2512.20581.pdf ---------------------------------------- bibcast.com